Method and apparatus for screening chemical compounds

ABSTRACT

Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.

This application is a continuation of application Ser. No. 10/227,552,filed Aug. 16, 2002, now abandoned, which is a continuation ofapplication Ser. No. 09/316,479, filed May 21, 1999, now abandoned,which is a continuation-in-part of application Ser. No. 09/300,335,filed Apr. 27, 1999, now abandoned, which is a continuation-in-part ofapplication Ser. No. 09/042,527, filed Mar. 16, 1998, now abandoned, anda continuation of International Application No. PCT/US99/05589, filedMar. 16, 1999.

FIELD OF THE INVENTION

The present invention relates to methods and apparatus for identifyingpharmacological agents useful for the diagnosis and treatment of diseaseby performing a variety of assays on cell extracts, cells or tissueswhere the measurement of biological activity involves the use of variousembodiments of a line-scan confocal imaging system and associated dataprocessing routines.

BACKGROUND OF THE INVENTION

There is currently a need in drug discovery and development and ingeneral biological research for methods and apparatus for accuratelyperforming cell-based assays. Cell-based assays are advantageouslyemployed for assessing the biological activity of chemical compounds andthe mechanism-of-action of new biological targets. In a cell-basedassay, the activity of interest is measured in the presence of bothcompeting and complementary processes. As pertains to chemical compoundscreening, information is available as to the specific activity of thecompound. For example, it is possible to assess not only whether acompound binds the target of the assay, but also whether it is anagonist or an antagonist of the normal activity of the target.Frequently, the target is a cell-surface receptor. In some signalingpathways, the member of the pathway of greatest potential therapeuticvalue is not the receptor but an intracellular signaling proteinassociated with the receptor. It is, therefore, desirable to developmethods to assay activity throughout the pathway, preferably in thecellular milieu.

In addition, there is a need to quickly and inexpensively screen largenumbers of chemical compounds. This need has arisen in thepharmaceutical industry where it is common to test chemical compoundsfor activity against a variety of biochemical targets, for example,receptors, enzymes and nucleic acids. These chemical compounds arecollected in large libraries, sometimes exceeding one million distinctcompounds. The use of the term chemical compound is intended to beinterpreted broadly so as to include, but not be limited to, simpleorganic and inorganic molecules, proteins, peptides, nucleic acids andoligonucleotides, carbohydrates, lipids, or any chemical structure ofbiological interest.

In the field of compound screening, cell-based assays are run oncollections of cells. The measured response is usually an average overthe cell population. For example, a popular instrument used for ionchannel assays is disclosed in U.S. Pat. No. 5,355,215. A typical assayconsists of measuring the time-dependence of the fluorescence of anion-sensitive dye, the fluorescence being a measure of theintra-cellular concentration of the ion of interest which changes as aconsequence of the addition of a chemical compound. The dye is loadedinto the population of cells disposed on the bottom of the well of amultiwell plate at a time prior to the measurement. In general, theresponse of the cells is heterogeneous in both magnitude and time. Thisvariability may obscure or prevent the observation of biologicalactivity important to compound screening. The heterogeneity may arisefrom experimental sources, but more importantly, heterogeneity isfundamental in any population of cells. Among others, the origin of thevariability may be a consequence of the life-cycle divergence among thepopulation, or the result of the evolutionary divergence of the numberof active target molecules. A method that mitigates, compensates for, oreven utilizes the variations would enhance the value of cell-basedassays in the characterization of the pharmacological activity ofchemical compounds.

Quantification of the response of individual cells circumvents theproblems posed by the non-uniformity of that response of a population ofcells. Consider the case where a minor fraction of the populationresponds to the stimulus. A device that measures the average responsewill have less sensitivity than one determining individual cellularresponse. The latter method generates a statistical characterization ofthe response profile permitting one to select the subset of activecells. Additional characterization of the population will enhance theinterpretation of the response profile.

Various measurement devices have been used in the prior art in anattempt to address this need. Flow-cytometer-based assays are widelypracticed and measure cell properties one at a time by passing cellsthrough a focused laser beam. Several disadvantages accompany thismethod. Most important to the pharmaceutical industry is that assays cannot readily be performed on compounds disposed in microtiter plates. Inaddition, the throughput is poor, typically 10-100 seconds per sample,the observation time of each cell is <1 ms, prohibiting kinetic assays,and finally, only the cell-averaged signal can be determined.

In addition, many assays require determination of the relative locationsof the fluorescence signals. Devices called scanning cytometers, asdisclosed in U.S. Pat. No. 5,107,422 and U.S. Pat. No. 5,547,849, arewidely used for imaging single cells. In order to gain acceptable speed,these devices operate at low (˜5-10 μm) resolution. Thus, these devicesoffer little advantage over flow cytometers for assays requiring spatialinformation on the distribution of the fluorescence signals.

An additional alternative technology is the fast-camera, full-fieldmicroscope. These devices have the ability to obtain images at aresolution and speed comparable to the present invention, on certainsamples. However, they are not confocal and are consequently susceptibleto fluorescence background and cannot be used to optically section thesample. In addition, simultaneous, multi-parameter data is not readilyobtained. In contrast to the prior art, the present invention can beused to perform multi-parameter fluorescence imaging on single cells andcell populations in a manner that is sufficiently rapid and versatilefor use in compound screening. Methods and apparatus are provided forobtaining and analyzing both the primary response of individual cellsand additional measures of the heterogeneity of the sample population.In addition, the locations of these multiple fluorophores can bedetermined with sub-cellular resolution. Finally, the present inventioncan be used to image rapidly changing events at video-rates. Togetherthese capabilities enable new areas of research into themechanism-of-action of drug candidates.

The present invention may also be employed in an inventivefluorescence-based biochemical assay, somewhat analogous to the surfacescintillation assay (“SSA”) which is among the more widely used methodsfor screening chemical compounds.

FIGS. 1A-1F depict the steps of a receptor-binding SSA. In FIG. 1A,soluble membranes 10 with chosen receptors 12 are added to a well 20containing a liquid 30. These membranes are isolated from cellsexpressing the receptors. In FIG. 1B, radio-labeled ligands 14 are addedto the well. The ligand is known to have a high binding affinity for themembrane receptors. The most common radio labels are ³H, ³⁵S, ¹²⁵I, ³³Pand ³²P. In FIG. 1C, beads 16 are added to the well. The beads arecoated with a material, such as wheat germ agglutinin, to which themembranes strongly adhere. The beads have a diameter of 3-8 μm and aremade of plastic doped with a scintillant. Alternatively, the order ofthe operations depicted in FIGS. 1B and 1C may be interchanged.

The radiolabels decay by emitting high energy electrons, or betaparticles, which travel approximately 1-100 μm before stopping,depending on the radio-isotope. If the radiolabels are bound to themembranes attached to the beads, the beta particles may travel into thebeads and cause bursts of luminescence. If the radio-labels aredispersed throughout the liquid, the emitted beta particles will notgenerally excite luminescence in the beads. In FIG. 1D, the luminescenceof the beads caused by decay of the radio labels is detected. In FIG.1E, a test compound 18 is added to the well. The purpose of the assay isto determine the extent to which this compound will displace theradio-labeled ligands. If radio-labeled ligands are displaced anddiffuse into the liquid, the luminescence of the beads will be reduced.In FIG. 1F, the luminescence of the beads is again detected. Bymeasuring the reduction in luminescence, the activity of the testcompound can be determined.

FIGS. 2A-2F depict an alternative embodiment of a receptor-binding SSA.This embodiment is essentially the same as that described in FIGS. 1A-1Fexcept that instead of using beads, the embodiment shown in FIGS. 2A-2Fuses a well bottom 22 made of plastic doped with scintillant and coatedwith a material to which the membranes adhere. Consequently, instead ofdetecting the luminescence of the beads, the embodiment shown in FIGS.2A-2F detects the luminescence of the well bottom.

FIGS. 3A-3D depict the steps of an embodiment of an enzyme SSA. In FIG.3A, scintillant-doped beads 40 with radio-labeled peptides 42 attachedthereto are added to a well 50 containing a liquid 60. In FIG. 3B, atest compound 44 is added to the well. In FIG. 3C, enzymes 46 are addedto the well. If not inhibited, enzymes 46 will cleave radio-labeledpeptides 42 from beads 40. As a result, the radio label will diffuseinto the solution, and radio-label decay will not produce luminescencein beads 40. If, on the other hand, test compound 44 inhibits enzymes46, typically by blocking the enzyme active site, enzymes 46 will notcleave the radio label and the decay of the radio label will produceluminescence in the beads. In FIG. 3D, the luminescence of the beads ismeasured and the activity of the test compound can be determined.

FIGS. 4A-4D depict an alternative embodiment of an enzyme SSA. In FIG.4A, radio-labeled peptides 42 are attached to a scintillant-doped wellbottom 52. In FIG. 4B, the test compound 44 is added to the well. InFIG. 4C, enzymes 46 are added to the well. In FIG. 4D, the luminescenceof the well bottom is measured to determine the activity of the testcompound.

The above examples illustrate the general principle of the SSA, namelythat the activity of interest is assayed by a change in the number ofradio labels within a radio-decay length of the scintillant. One of theattractions of SSAs is that the radio labels not attached to thescintillant need not be removed from the well in a wash step. That isSSAs are homogeneous assays.

A radioimmunoassay (RIA) is a specific form of a receptor binding assayin which the receptor is an antibody and the ligand is most often anatural or synthetic peptide, protein, carbohydrate or small organicmolecule. RIAs are an indirect method for measuring the concentration ofligand in any prepared sample, most often a biological sample such asplasma, cerebrospinal fluid, urine, or cellular extract. In a standardRIA, the antibody has a specific affinity for the ligand and the assaycontains the antibody, a fixed concentration of radiolabeled ligand andan unknown concentration of non-labelled ligand. The concentration ofthe unlabelled ligand is determined by the degree to which it binds tothe antibody and thereby blocks binding of the labelled ligand. RIAs aremost often performed as heterogenous assays that require the separationof bound ligand from unbound ligand with a wash step. RIAs have alsobeen developed using an SSA configuration in which the antibody receptoris attached to a scintillant filled bead and the wash step iseliminated.

SSAs and RIAs, however, suffer from a number of disadvantages. First,these assays require handling radioactive material, which is bothexpensive and time consuming. Second, these assays are only effective inlarge wells. The rate of luminescence emission from the beads or wellbottoms is proportional to the beta particle emission rate. A typical ³Hassay yields less than one detected photon per ³H decay. To increase thespeed of the assay, the quantity of radio-labeled ligand must beincreased, and correspondingly the quantities of membranes, beads andtest compound. In order to perform a tritium SSA in 10-60 seconds, 10⁷beads must be used. This quantity of beads requires a well ofapproximately 150 μL. SSAs are not effective in the μL-volume wellsdesirable for screening large numbers of compounds.

As described below, the present invention, inter alia, replaces theradio-labeled ligands of the SSA and the RIA with fluorescent-labeledligands. In so doing, it introduces a homogenous format for the RIA andit advantageously retains the homogeneous format of the SSA. This isparticularly important in μL-volume wells, for which surface tensionrenders washing impractical. However, in a homogeneous format,fluorescence can be a problem as can be illustrated with thereceptor-binding assay. When the test compound is added, somefluorescent-labeled ligands are displaced and diffuse freely throughoutthe volume of the well, while others remain attached to the membranes.It is the fluorescence of the fluorescent-labeled ligands attached tothe membranes that is used to determine the activity of the testcompound. If the fluorescence is detected from the entire well, however,the emission from the fluorescent-labeled ligands in the volume of thewell will obscure the emission from the fluorescent-labeled ligandsattached to the membranes.

One method addressing this problem is described in U.S. Pat. No.5,355,215 to Schroeder et al. and shown in FIGS. 5A and 5B. According tothe Schroeder et al. method, the samples are illuminated by a beam 134of light that is directed at the bottom of the well at an oblique angle,shown as A in FIG. 5, so that it does not illuminate the entire well. Inaddition, while the beam illuminates area 114′, fluorescence is detectedonly from area 114 a which is under the well volume which receives theleast amount of illumination.

The Schroeder et al. method, however, suffers from a number ofdisadvantages. First, because it detects only a small portion of thewell bottom, the Schroeder et al. method can only be performed with asufficient degree of accuracy on fairly large wells. It is not suitableto image samples disposed in the approximately 1-mm diameter wells of a1536-well plate. Second, the geometric constraints of the angledillumination preclude the use of high numerical aperture collectionoptics, necessary to achieve sufficient sensitivity and resolution toimage micron-sized objects, such as individual cells, at the bottom ofthe well.

Another approach to this problem uses a point-scan microscope. Forexample, in U.S. Pat. No. 5,547,849 to Baer et al., the use of apoint-scan confocal system is taught. Baer et al. teach a method toincrease the slow speed of image acquisition, inherent in point-scanconfocal techniques, by sacrificing spatial resolution. If, for example,one expands the diameter of the illumination beam on the sample by afactor of 10, then the illumination area is increased 100-fold,permitting one to scan 100-times faster, under certain conditions. Thespeed increase is achieved, however, at the expense of resolution.Further, the detection devices appropriate to said scanning method, asdisclosed in the '849 patent, are inferior, principally in terms ofsensitivity, to those advantageously used in the present invention.Finally, the degree of background rejection is diminished along with theresolution. Thus the device disclosed in the '849 patent has lessersensitivity, higher background and lower resolution than the presentinvention, all of which are important in the present application.

The present invention includes novel embodiments of a line-scan confocalmicroscope. Line-scan confocal microscopes are known in art. Tworepresentative embodiments are the system disclosed by White et al. inU.S. Pat. No. 5,452,125 and that published by Brakenhoff and Visscher inJ. Microscopy 171 17-26 (1993), shown in FIG. 7. Both use a scanningmirror to sweep the illumination across the sample. The same mirrorde-scans the fluorescence radiation. After spatial filtering with aslit, the fluorescence is rescanned for viewing by eye. The use of theoscillating mirror enables these microscopes to rapidly scan afield-of-view. Line illumination is advantageous principally inapplications requiring rapid imaging. The potential speed increaseinherent in the parallelism of line illumination as compared to pointillumination is, however, only realized if the imaging system is capableof detecting the light emitted from each point of the sample along theillumination line, simultaneously. An essential feature of the disclosedapparatus is the use of a detection device having manifold, independentdetection elements in a plane conjugate to the object plane.

According to the present invention, the sample must lie in a “plane”,where the depth-of-field of the imaging system determines the precisionof “planarity”. In a preferred embodiment, the imaged area is 1 mm² andthe depth-of-field is 10 μm. Thus, if the entire field is to be in focussimultaneously, the sample must be flat to 1 part in 100. This is trueof many sample substrates (e.g. microtiter plates) over a local area(such as the central area of the well bottom). It is not practical,however, to require that the sample substrate be flat over its entiresurface. For a microtiter plate having an extent of ˜100 mm, planarityof 1 part in 10,000 would be necessary.

The present invention provides for an optical autofocus system whichmaintains in “focus” the portion of the sample substrate being imaged.An optical autofocus mechanism has the advantage of being fast and beingoperational with non-conducting substrates such as plastic microtiterplates and microscope slides. Advantageously, this focus mechanismoperates with negligible delay, that is, the response time of thefocusing mechanism is short relative to the image acquisition-time,preferably a fraction of a second. Optically-based autofocus mechanismssuitable for the present application are known. For example, anastigmatic-lens-based system for the generation of a position errorsignal suitable for servo control is disclosed in Applied Optics 23565-570 (1984), and a focus error detection system utilizing a “skewbeam” is disclosed in SPIE 200 73-78 (1979). In a preferred embodimentof the present invention, the sample substrate is a microtiter plate. Inthis case, the preferred means of accomplishing the focusing dependsfurther on the properties of the plate. If the thickness of the platebottom were uniform to within a fraction of the depth-of-focus, then afocusing mechanism that maintained the plate bottom at a constant offsetfrom the object plane would be adequate. Presently, commonly usedmicrotiter plates are not sufficiently uniform. Thus, the focusingmechanism must track the surface on which the sample resides, which istypically the inside of the microtiter plate well. An aspect of thepresent invention is a novel autofocus mechanism for rapidly focusing ona discontinuous surface, such as the well bottom of a microtiter plate.

There is, therefore, a need for a method and apparatus for screeninglarge numbers of chemical compounds accurately, quickly andinexpensively, in a homogeneous format. In addition, there is a need fora methods and apparatus that can perform multi-parameter fluorescenceimaging with sufficient resolution to image individual cells andsub-cellular events. There is also a need for an imaging system that canadditionally monitor a statistically significant population of cells atvideo-rates.

SUMMARY OF THE INVENTION

The present invention relates to a line-scan confocal microscope and theuse of a line-scan confocal imaging (LCI) system to assay biologicalactivity.

In a preferred embodiment, the line-scan confocal imaging system employslaser light sources of multiple wavelengths for illuminating the sampleand exciting fluorophores to emit electromagnetic energy. Thesewavelengths include the ultraviolet spectrum as well as the visible.

The present invention is able to conduct a rapid series of assays onmicro-well plates by use of an autofocus capability which allows the LCIsystem to rapidly move from one well to another but not lose theadvantage of the confocal microscope's inherent ability to resolve thinoptical sections.

In various embodiments of the present invention the sample is moved toeffect a scan of the line of illumination over the sample. In otherembodiments, an oscillating mirror is used to produce a rapidly movingline of illumination effecting a scan of a sample which remains at afixed position. By way of example, images can be obtained at a rate ofup to 50 frames per second.

The present invention preferably provides for integrated dispensingallowing the addition of substances to initiate rapidly changingbiological events, such as the propagation of an action potential innerve or muscle cells.

The present invention preferably makes use of a multi-element solidstate detection device such as a charged coupled device (CCD). Thisdevice is preferably read continuously. In a preferred embodiment, thepresent invention uses a rectangular CCD which avoids the need for afull two dimensional detector and allows higher read speeds. Inaddition, a larger effective field-of-view is achievable in thestage-scanning embodiment.

The present invention also provides in a preferred embodiment, acapability to conduct specialized data analysis simultaneously with dataacquisition to allow it to operate in a high-throughput screening mode.

This invention provides methods of performing a wide variety ofbiological assays utilizing fluorescence. In one embodiment the targetof interest may be in a fixed or live cell or in a subcellular organelleor on the cell membrane. These assays involve the determination of oneor more parameters which requires the excitation of one or morefluorescent labels which are, in general, sensitive to differentwavelengths of incident light. In addition these assays require thesimultaneous and precise imaging of the emitted light at one or morewavelengths from which the location in two or three dimensions and theintensity of the fluorescently labeled species and their correlationsare determined.

In addition, this invention provides methods to perform assays whichrequire either a single imaging of a response, by means of fluorescentemission, or rapidly repeated imaging of the same area or cell. Invarious embodiments, imaging is performed at rates as high as 50 framesper second. This ability to image rapidly, in multiple wavelengths andwith high spatial resolution allows the present invention to performassays that could not previously be performed or to perform them in asuperior manner.

The present invention relates to several methods for screening chemicalcompounds and for performing many types of assays involving the use offluorophores or fluorescent probes. In general these assays andscreening procedures involve the use of a test compound and reagentssome or all of which are intrinsically fluorescent, tagged withfluorescent labels or are metabolized into fluorescent product. The testcompound and the reagents may be combined in a variety of ways.

In one embodiment, the reagents are added to a well containing a liquid.This may be a single well or one of many wells on a multiwell plate. Thebiological activity of interest is determined by the presence or absenceof fluorophores disposed on the bottom of the well or on the surface ofbeads disposed on the bottom of the well as measured with a line-scanconfocal microscope. This embodiment has in common with the SSA formatthe determination of activity from the localization of the detectedspecies. In the case of the SSA, the localization is proximal to thescintillant. In the present method, the localization is to a region ofthe well, preferably the bottom. In the case of the SSA, sensitivity tothe proximal species is determined by the decay length of the betaparticles. In the present method, sensitivity to the localizedfluorophore is determined by the optical-sectioning depth of theconfocal microscope.

In addition, the present invention can perform high throughput assaysrequiring scanning multiple samples in a rapid and automatic manner.These samples may be individual micro-wells and may involve wellscontaining a liquid and live or fixed cells or components of cells. Thepresent invention also provides environmental controls required toretain liquid samples or sustain live cells during the analysis.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other objects, features and advantages of the invention willbe more readily apparent from the following detailed description inwhich:

FIGS. 1A-1F illustrate a first receptor-binding SSA.

FIGS. 2A-2F illustrate a second receptor-binding SSA.

FIGS. 3A-3D illustrate a first enzyme SSA.

FIGS. 4A-4D illustrate a second enzyme SSA.

FIGS. 5A and 5B are schematic views of a prior art apparatus for imagingsamples disposed on the bottom of a well.

FIG. 6 is a schematic view of a first embodiment of a line-scan confocalmicroscope used to image samples according to the present invention.

FIG. 7 is a schematic view of a prior art microscope.

FIGS. 8A and 8B are, respectively, a top view and a side view of the raypath of a multicolor embodiment of the present invention, without ascanning mirror. FIG. 8C is a top view of the ray path of a single beamautofocus.

FIGS. 9A and 9B are, respectively, a top view and a side view of the raypath of the multicolor embodiment of the present invention with thescanning mirror. FIG. 9C is a top view of the ray path of the singlebeam autofocus.

FIG. 10 is a side view of the two beam autofocus system.

FIGS. 11A-11C illustrates the rectangular CCD camera and readoutregister,

FIGS. 12A and 12B are cross-sectional views of ray paths formed by theline-scan confocal microscope in the present invention employingconventional dark-field imaging.

FIGS. 13A and 13B are cross-sectional views of ray paths formed by theline-scan confocal microscope in the present invention using inversedark-field imaging.

FIG. 14 is a cross-sectional view of ray paths formed by the line-scanconfocal microscope in the present invention using inverse dark-fieldimaging, where an area larger than the diffraction-limited area of thesample plane is illuminated.

FIGS. 15A-15F illustrate a first embodiment of a receptor-binding assayaccording to the present invention.

FIGS. 16A-16F illustrates a second embodiment of a receptor-bindingassay according to the present invention.

FIGS. 17A-17D illustrate a first embodiment of an enzyme assay accordingto the present invention.

FIGS. 18A-18D illustrate a second embodiment of an enzyme assayaccording to the present invention.

FIGS. 19A-19D shows a transcription factor translocation assay.

FIGS. 20A-20D shows a translocation assay data analysis.

FIGS. 21A-21E shows another data analysis.

FIGS. 22A-22P shows neuroblastoma cell calcium response to Carbachol.

FIGS. 23A-23H shows neuroblastoma cell calcium response to 50 mM KCl.

FIGS. 24A-24C shows homogeneous live cell receptor binding assay.

FIGS. 25A-25D shows homogeneous live cell receptor binding assay.

FIGS. 26A-26D shows homogeneous live cell receptor binding assay withCy3 labeled ligand.

FIGS. 27A-27D shows 4 μm diameter silica beads with varying numbers ofCy5 labels.

FIGS. 28A-28E shows the data from the translocation assay, ion channelassay and cell surface receptor binding as graphs.

DETAILED DESCRIPTION OF THE INVENTION

All patent applications, publications, and other references that arelisted herein are hereby incorporated by reference in their entireties.

The present invention is useful for identifying pharmacological agentsfor the treatment of disease. It provides a high throughput method forconducting a wide variety of

biological assays where one or more fluorescent reagents are employed tomeasure a biological response. Such assays can be conducted on chemicalcompounds or any molecule of biological interest, included but notlimited to drug candidates, such as those found in combinatoriallibraries. In addition, this invention provides a method for thediagnosis of pathological states from cell and tissue samples. Thisinvention also provides a method for profiling multiple biologicalresponses of drug candidates on whole cells using fluorescent reagents.

The techniques of the present invention may be used in assays in whichdata is acquired on individual cells, on a cellular or sub-cellularlevel, sufficiently rapidly so as to permit the acquisition of such dataon a sufficient number of cells to constitute a statistically meaningfulsample of the cell population. The present invention is able to makesimultaneous measurements on multiple parameters and is also able tocorrelate multiple signals from individual cells. It may therefore beemployed to assay heterogeneous cellular responses and to assayresponses confined to a small subset of cells.

In addition, the present invention can image the simultaneous activationof multiple signal pathways and can correlate multiple signalssimultaneously and over time. This capability is vital when the temporalresponse of individual cells or a comparison of the temporal response ofindividual cells is required for the specific assay.

In addition, the present invention can image fluorescent signals fromthe confocal plane of cells in the presence of unbound fluorophore or inthe presence of intrinsically fluorescent chemical compounds, includingpotential drug candidates.

These assays may make use of any known fluorophore or fluorescent labelincluding but not limited to fluorescein, rhodamine, Texas Red, AmershamCorp. stains Cy3, Cy5, Cy5.5 and Cy7, Hoechst's nuclear stains andCoumarin stains. (See Haugland R. P. Handbook of Fluorescent Probes andResearch Chemicals 6^(th) Ed., 1996, Molecular Probes, Inc., Eugene,Oreg.)

These assays include but are not limited to receptor-binding assays,assays of intra-cellular electric potential or pH, assays of ionconcentrations, enzyme activity assays, trafficking assays, kineticimaging assays and assays of rare cellular events.

Receptor-binding and enzyme activity assays may be bead-based orcell-based assays. Some examples of bead-based assays are described inWO 98/55866. However, the method described therein makes use of pointscan confocal technology and the present linescan confocal imagingsystem would have a significant advantage in terms of rate of dataacquisition.

Optical Configuration

FIG. 6 shows a first embodiment of the present invention. The microscopecomprises a source 400 or 410 of electromagnetic radiation for example,in the optical range, 350-750 nm, a cylindrical lens 420, a first slitmask 430, a first relay lens 440, a dichroic mirror 450, an objectivelens 470, a microtiter plate 480 containing a two-dimensional array ofsample wells 482, a tube lens 490, a filter 500, a second slit mask 510and a detector 520. These elements are arranged along optical axis OAwith slit apertures 432, 512 in masks 430, 510 extending perpendicularto the plane of FIG. 6. The focal lengths of lenses 440, 470 and 490 andthe spacings between these lenses as well as the spacings between mask430 and lens 440, between objective lens 470 and microtiter plate 480and between lens 490 and mask 510 are such as to provide a confocalmicroscope. In this embodiment, electromagnetic radiation from a lamp400 or a laser 410 is focused to a line using a cylindrical lens 420.The shape of the line is optimized by a first slit mask 430. The slitmask 430 is depicted in an image plane of the optical system, that is ina plane conjugate to the object plane. The illumination stripe formed bythe aperture 432 in the slit mask 430 is relayed by lens 440, dichroicmirror 450 and objective lens 470 onto a microtiter plate 480 whichcontains a two-dimensional array of sample wells 482. For convenience ofillustration, the optical elements of FIG. 6 are depicted incross-section and the well plate in perspective. The projection of theline of illumination onto well plate 480 is depicted by line 484 and isalso understood to be perpendicular to the plane of FIG. 6. As indicatedby arrows A and B, well plate 480 may be moved in two dimensions (X, Y)parallel to the dimensions of the array by means not shown.

In an alternative embodiment, the slit mask 430 resides in a Fourierplane of the optical system, that is in a plane conjugate to theobjective back focal plane (BFP) 460. In this case the aperture 432 liesin the plane of the figure, the lens 440 relays the illumination stripeformed by the aperture 432 onto the back focal plane 460 of theobjective 470 which transforms it into a line 484 in the object planeperpendicular to the plane of FIG. 6.

In an additional alternative embodiment the slit mask 430 is removedentirely. According to this embodiment, the illumination source is thelaser 410, the light from which is focused into the back focal plane 460of the objective 470. This can be accomplished by the combination of thecylindrical lens 420 and the spherical lens 440 as shown in FIG. 6, orthe illumination can be focused directly into the plane 460 by thecylindrical lens 420.

An image of the sample area, for example a sample in a sample well 482,is obtained by projecting the line of illumination onto a plane withinthe sample, imaging the fluorescence emission therefrom onto a detector520 and moving the plate 480 in a direction perpendicular to the line ofillumination, synchronously with the reading of the detector 520. In theembodiment depicted in FIG. 6, the fluorescence emission is collected bythe objective lens 470, projected through the dichroic beamsplitter 450,and imaged by lens 490 through filters 500 and a second slit mask 510onto a detector 520, such as is appropriate to a confocal imaging systemhaving an infinity-corrected objective lens 470. The dichroicbeamsplitter 450 and filter 500 preferentially block light at theillumination wavelength. The detector 520 illustratively is a camera andmay be either one dimensional or two dimensional. If a one dimensionaldetector is used, slit mask 510 is not needed. The illumination,detection and translation procedures are continued until the prescribedarea has been imaged. Mechanical motion is simplified if the sample istranslated at a continuous rate. Continuous motion is most useful if thecamera read-time is small compared to the exposure-time. In a preferredembodiment, the camera is read continuously. The displacement d of thesample during the combined exposure-time and read-time may be greaterthan or less than the width of the illumination line W, exemplarily 0.5W≦d≦5 W. All of the wells of a multiwell plate can be imaged in asimilar manner.

Alternatively, the microscope can be configured to focus a line ofillumination across a number of adjacent wells, limited primarily by thefield-of-view of the optical system. Finally, more than one microscopecan be used simultaneously.

The size and shape of the illumination stripe 484 is determined by thewidth and length of the Fourier transform stripe in the objective lensback focal plane 460. For example, the length of the line 484 isdetermined by the width of the line in 460 and conversely the width in484 is determined by the length in 460. For diffraction-limitedperformance, the length of the illumination stripe at 460 is chosen tooverfill the objective back aperture. It will be evident to one skilledin the art that the size and shape of the illumination stripe 484 can becontrolled by the combination of the focal length of the cylindricallens 420 and the beam size at 420, that is by the effective numericalaperture in each dimension, within the restrictions imposed byaberrations in the objective, and the objective field of view.

The dimensions of the line of illumination 484 are chosen to optimizethe signal to noise ratio. Consequently, they are sample dependent.Depending on the assay, the resolution may be varied betweendiffraction-limited, i.e., less than 0.5 μm, and approximately 5 μm. Thebeam length is preferably determined by the objective field of view,exemplarily between 0.5 and 1.5 mm. A Nikon ELWD, 0.6 NA, 40× objective,for example, has a field of view of approximately 0.75 mm. Thediffraction-limited resolution for 633 nm radiation with this objectiveis approximately 0.6 μm or approximately 1100 resolution elements.

The effective depth resolution is determined principally by the width ofaperture 512 in slit mask 510 or the width of the one dimensionaldetector and the image magnification created by the combination of theobjective lens 470 and lens 490. The best depth resolution of a confocalmicroscope approaches 1 μm. In the present application, a depthresolution of 5-10 μm may be sufficient or even advantageous.

For example, when the sample of interest, such as a live cell, containsinsufficient fluorophores in a diffraction-limited volume to permit anadequate signal-to-noise image in a sufficiently brief image-acquisitiontime, it is advantageous to illuminate and collect the emission from alarger than diffraction-limited volume. A similar situation prevails inthe case of video-rate kinetics studies of transient events such asion-channel openings. Practically, this is accomplished by underfillingthe back aperture of the objective lens, which is equivalent toincreasing the diameter of the illumination aperture. The effectivenumerical aperture (“NA”) of the illumination is less than the NA of theobjective. The fluorescence emission is, however, collected with thefull NA of the objective lens. The width of aperture 512 must beincreased so as to detect emission from the larger illumination volume.At an aperture width a few times larger than the diffraction limit,geometrical optics provides an adequate approximation for the size ofthe detection-volume element:

Lateral Width: a_(d)=d_(d)/M,

Axial Width: Z_(d)=√2 a _(d)/tan α,

where M is the magnification, d_(d) is the width of aperture 512 and αis the half-angle subtended by the objective 470. It is an importantpart of the present invention that the illumination aperture 432 or itsequivalent in the embodiment having no aperture and the detectionaperture 512 be independently controllable.

Multi-Wavelength Configuration

An embodiment enabling multi-wavelength fluorescence imaging ispreferred for certain types of assays. It is generally advantageous andoften necessary that two or more measurements be made simultaneouslysince one important parameter in a biological response is time.

The number of independent wavelengths or colors will depend on thespecific assay being performed. In one embodiment three illuminationwavelengths are used. FIGS. 8A and 8B depict the ray paths in athree-color line-scan confocal imaging system, from a top view and aside view respectively. In general, the system comprises several sourcesS_(n) of electromagnetic radiation, collimating lenses L_(n), andmirrors M_(n) for producing a collimated beam that is focused bycylindrical lines CL into an elongated beam at first spatial filter SF₁,a confocal microscope between first spatial filter SF₁, and secondspatial filter SF₂ and an imaging lens IL, beamsplitters DM₁ and DM₂ anddetectors D_(n) for separating and detecting the different wavelengthcomponents of fluorescent radiation from the sample. Spatial filters SF,and SF₁ and SF₂ preferably are slit masks.

In particular, FIG. 8A depicts sources, S₁, S₂ and S₃, for colors λ₁, λ₂and λ₃, and lenses L₁, L₂ and L₃ that collimate the light from therespective sources. Lenses L₁, L₂ and L₃, preferably are adjusted tocompensate for any chromaticity of the other lenses in the system.Mirrors M₁, M₂ and M₃ are used to combine the illumination colors fromsources Sn. The mirrors M₂ and M₁ are partially transmitting, partiallyreflecting and preferentially dichroic. M₂, for example, shouldpreferentially transmit λ₃, and preferentially reflect λ₂. It is thuspreferential that λ₃ be greater than λ₂.

Operation of the microscope in a confocal mode requires that thecombined excitation beams from sources S_(n) be focused to a “line”, oran highly eccentric ellipse, in the object plane OP. As discussed inconnection to FIG. 6 above, a variety of configurations may be used toaccomplish this. In the embodiment depicted in FIG. 8, the combinedillumination beams are focused by cylindrical lens CL into an elongatedellipse that is coincident with the slit in the spatial filter SF₁. Asdrawn in FIGS. 8A and 8B, the slit mask SF₁ resides in an image plane ofthe system, aligned perpendicular to the propagation of the illuminationlight and with its long axis in the plane of the page of FIG. 8A. Thelenses TL and OL relay the illumination line from the plane containingSF₁ to the object plane OP. A turning mirror, TM, is for convenience. Inanother embodiment, DM₃ is between TL and OL and CL focuses theillumination light directly into the BFP. Other embodiments will beevident to one skilled in the art.

Referring to FIG. 8B, the light emitted by the sample and collected bythe objective lens, OL, is imaged by the tube lens, TL, onto the spatialfilter, SF₂. SF₂ is preferentially a slit aligned so as to extendperpendicular to the plane of the page. Thus, the light passed by filterSF₂ is substantially a line of illumination. SF₂ may be placed in theprimary image plane or any plane conjugate thereto. DM₃ is partiallyreflecting, partially transmitting and preferably “multichroic”.Multi-wavelength “dichroic” mirrors, or “multichroic” mirrors can beobtained that preferentially reflect certain wavelength bands andpreferentially transmit others.

δλ₁ will be defined to be the fluorescence emission excited by λ₁. Thiswill, in general, be a distribution of wavelengths somewhat longer thanλ₁. δλ₂ and δλ₃ are defined analogously. DM₃ preferentially reflectsλ_(n), and preferentially transmits δλ_(n), n=1,2,3. The lighttransmitted by SF₂ is imaged onto the detection devices, which reside inplanes conjugate to the primary image plane. In FIG. 8A, an image of thespatial filter SF₂ is created by lens IL on all three detectors, D_(n).This embodiment is preferred in applications requiring near-perfectregistry between the images generated by the respective detectors. Inanother embodiment, individual lenses IL_(n) are associated with thedetection devices, the lens pairs IL and IL_(n) serving to relay theimage of the spatial filter SF₂ onto the respective detectors D_(n). Thelight is split among the detectors by mirrors DM₁ and DM₂. The mirrorsare partially transmitting, partially reflecting, and preferentiallydichroic. DM₁ preferentially reflects δλ₁ and preferentially transmitsδλ₂ and δλ₃. The blocking filter, BF₁, preferentially transmits δλ₁effectively blocking all other wavelengths present. DM₂ preferentiallyreflects δλ₂ and preferentially transmits δλ₃. The blocking filters, BF₂and BF₃, preferentially transmit δλ₂ and δλ₃ respectively, effectivelyblocking all other wavelengths present.

Scanning Mirror Configuration

In some embodiments of this invention, rapid data acquisition requiresframing images at video rates. Video-rate imaging generally refers to 30or 60 frames per second. In the present use, it is intended to connoteframe rates with an order-of-magnitude of 30 Hz. In a preferredembodiment, video-rate imaging is achieved by illuminating along onedimension of the sample plane and scanning the illumination beam in thedirection perpendicular thereto so as to effect a relative translationof the illumination and sample. The scanning stage is generally massive.Consequently, it cannot be moved sufficiently rapidly.

FIG. 9 depicts an embodiment of the invention utilizing a scanningmirror, SM. The mirror is advantageously placed in a plane conjugate tothe objective back focal plane (BFP): A rotation in the BFP (or a planeconjugate thereto) effects a translation in the object plane (OP) andits conjugate planes. The full scan range of SM need only be a fewdegrees for typical values of the focal lengths of the lenses RL₁ andRL₂. As shown in FIG. 9, this lens pair images the BFP onto the SM at amagnification of one, but a variety of magnifications can beadvantageously used. The limiting factors to the image acquisition rateare the camera read-rate and the signal strength. In the imaging modedescribed above, data can be acquired continuously at the cameraread-rate, exemplarily 1 MHz. With a scanning mirror, it is preferableto acquire data uni-directionally. The idealized scanning motionallowing one to acquire data continuously is the sawtooth. In practice,the combination of turn-around and return scan times will constitute˜⅓-⅔ of the scan period. Assuming 50% dead-time, a mirror oscillationfrequency of 50 Hz and a pixel acquisition rate of 1 MHz, ˜10,000 pixelswould be acquired per frame at 50 frames per second, which is sufficientto define and track individual objects, such as cells, from frame toframe. 10⁴ pixels per image is, however, 10²-times fewer than wasgenerally considered above. Depending on the application, it isadvantageous to acquire relatively smaller images at high resolution,e.g. 50-μm×50-μm at 0.5-μm×0.5-μm pixelation, or relatively largerimages at lower resolution, e.g. 200-μm×200-μm at 2-μm pixelation.

Autofocus

According to the present invention, the sample must lie in the objectplane of an imaging system. Accordingly, the invention provides anautofocus mechanism that maintains the portion of the sample in thefield-of-view of the imaging system within the object plane of thatsystem. The precision of planarity is determined by the depth-of-fieldof the system. In a preferred embodiment, the depth-of-field isapproximately 10 μm and the field-of-view is approximately 1 mm².

The disclosed autofocus system operates with negligible delay, that is,the response time is short relative to the image acquisition-time,exemplarily 0.01-0.1 s. In addition, the autofocus light source isindependent of the illumination light sources and the sample properties.Among other advantages, this configuration permits the position of thesample carrier along the optical axis of the imaging system to bedetermined independent of the position of the object plane.

One embodiment of a single-beam autofocus is provided in FIGS. 8 and 9,where a separate light source, S₄ of wavelength λ₄, and detector D₄ areshown. The wavelength λ₄ is necessarily distinct from the samplefluorescence, and preferentially a wavelength that cannot exciteappreciable fluorescence in the sample. Thus, λ4 is preferentially inthe near infrared, exemplarily 800-1000 nm. The partially transmitting,partially reflecting mirror, DM₄, is preferentially dichroic, reflectingλ₄ and transmitting λ_(n) and δλ_(n), n, n=1,2,3. Optically-basedautofocus mechanisms suitable for the present application are known. Forexample, an astigmatic-lens-based system for the generation of aposition error signal suitable for servo control is disclosed in AppliedOptics 23 565-570 (1984). A focus error detection system utilizing a“skew beam” is disclosed in SPIE 200 73-78 (1979). The latter approachis readily implemented according to FIGS. 8 and 9, where D₄ is a splitdetector.

For use with a microtiter plate having a sample residing on the wellbottom, the servo loop must, however, be broken to move between wells.This can result in substantial time delays because of the need torefocus each time the illumination is moved to another well.

Continuous closed-loop control of the relative position of the sampleplane and the object plane is provided in a preferred embodiment of thepresent invention, depicted in FIG. 10. This system utilizes twoindependent beams of electromagnetic radiation. One, originating fromS₅, is focused on the continuous surface, exemplarily the bottom of amicrotiter plate. The other, originating from S₄, is focused on thediscontinuous surface, exemplarily the well bottom of a microtiterplate. In one embodiment, the beams originating from S₄ and S₅ havewavelengths λ₄ and λ₅, respectively. λ₄ is collimated by L₄, aperturedby iris I₄, and focused onto the discontinuous surface by the objectivelens OL. λ₅, is collimated by L₅, apertured by iris I₅, and focused ontothe continuous surface by the lens CFL in conjunction with the objectivelens OL. The reflected light is focused onto the detectors D₄ and D₅ bythe lenses IL₄ and IL₅, respectively. The partially transmitting,partially reflecting mirror, DM₄, is preferentially dichroic, reflectingλ₄ and λ₅ and transmitting λ_(n) and δλ_(n), n=1,2,3. The mirrors, M₄,M₅ and M₆, are partially transmitting, partially reflecting. In the casethat λ₄ and λ₅ are distinct, M₆ is preferentially dichroic.

According to the embodiment wherein the sample resides in a microtiterplate, λ₄ is focused onto the well bottom. The object plane can beoffset from the well bottom by a variable distance. This is accomplishedby adjusting L₄ or alternatively by an offset adjustment in the servocontrol loop. For convenience of description, it will be assumed that λ₄focuses in the object plane.

The operation of the autofocus system is as follows. If the bottom ofthe sample well is not in the focal plane of objective lens OL, detectorD₄ generates an error signal that is supplied through switch SW to the Zcontrol. The Z control controls a motor (not shown) for moving themicrotiter plate toward or away from the objective lens. Alternatively,the Z control could move the objective lens. If the bottom PB of themicrotiter plate is not at the focal plane of the combination of thelens CFL and the objective lens OL, detector D₅ generates an errorsignal that is applied through switch SW to the Z control. An XY controlcontrols a motor (not shown) for moving the microtiter plate in theobject plane OP of lens OL.

As indicated, the entire scan is under computer control. An exemplaryscan follows: At the completion of an image in a particular well, thecomputer operates SW to switch control of the servo mechanism from theerror signal generated by D₄ to that generated by D₅; the computer thendirects the XY control to move the plate to the next well, after whichthe servo is switched back to D₄.

The “coarse” focusing mechanism utilizing the signal from the bottom ofthe plate is used to maintain the position of the sample plane to withinthe well-to-well variations in the thickness of the plate bottom, sothat the range over which the “fine” mechanism is required to search isminimized. If, for example, the diameter of the iris I₅ is 2 mm and IL₅is 100 mm, then the image size on the detector will be ˜100 μm.Similarly, if the diameter of the iris I₄ is 0.5 mm and IL₄ is ˜100 mm,then the image size on the detector will be ˜400 μm. The latter ischosen to be less sensitive so as to function as a “coarse” focus.

As with the single-beam embodiment described above, the wavelengths λ₄and λ₅ are necessarily distinct from the sample fluorescence, andpreferentially wavelengths that cannot excite appreciable fluorescencein the sample. Thus, λ₄ and λ₅ are preferentially in the near infrared,such as 800-1000 nm. In addition, the two wavelengths are preferablydistinct, for example λ₄=830 nm, λ₅=980 nm.

In an alternative embodiment of two-beam autofocus, λ₄=λ₅ and the twobeams may originate from the same source. Preferentially, the two beamsare polarized perpendicular to one another and M₆ is a polarizingbeamsplitter.

Pseudo-closed loop control is provided in the preferred embodiment ofsingle-beam autofocus which operates as follows. At the end of a scanthe computer operates SW to switch control to a sample-and-hold devicewhich maintains the Z control output at a constant level while the plateis moved on to the next well after which SW is switched back to D₄

Detection Devices

An essential feature of the disclosed apparatus is the use of adetection device having manifold, independent detection elements in aplane conjugate to the object plane. As discussed above, lineillumination is advantageous principally in applications requiring rapidimaging. The potential speed increase inherent in the parallelism ofline illumination as compared to point illumination is, however, onlyrealized if the imaging system is capable of detecting the light emittedfrom each point of the sample along the illumination line,simultaneously.

It is possible to place a charge-coupled device (CCD), or other camera,at the output of the prior art imaging systems described above (White etal., U.S. Pat. No. 5,452,125 and Brakenhoff and Visscher, J. Microscopy171 17-26 (1993)). The resulting apparatus has three significantdisadvantages compared to the present invention. One is the requirementof rescanning the image onto the two-dimensional detector, which addsunnecessary complexity to the apparatus. Another is the requirement of afull two-dimensional detector having sufficient quality over the 1000pixel×1000 pixel array that typically constitutes the camera. The thirddisadvantage is the additional time required to read the full image fromthe two-dimensional device.

The present invention is designed to avoid these disadvantages andoptimize not only imaging speed, within the constraints ofhigh-sensitivity and low-noise detection, but also throughput. Oneembodiment uses a continuous-read line-camera, and in a preferredembodiment a rectangular CCD is used as a line-camera. Both embodimentshave no dead-time between lines within an image or between images. Anadditional advantage of the present invention is that a larger effectivefield-of-view is achievable in the stage-scanning embodiment, discussedbelow.

The properties required of the detection device can be further clarifiedby considering the following preferred embodiment. The resolution limitof the objective lens is <1 μm, typically ˜0.5 μm, and the detectorcomprises an array of ˜1000 independent elements. Resolution,field-of-view (FOV) and image acquisition-rate are not independentvariables, necessitating compromise among these performance parameters.In general, the magnification of the optical system is set so as toimage as large a FOV as possible without sacrificing resolution. Forexample, a ˜1 mm field-of-view could be imaged onto a 1000-element arrayat 1-μm pixelation. If the detection elements are 20-μm square, then thesystem magnification would be set to 20×. Note that this will not resultin 1-μm resolution. Pixelation is not equivalent to resolution. If, forexample, the inherent resolution limit of the objective lens is 0.5 μmand each 0.5 μm×0.5 μm region in the object plane is mapped onto apixel, the true resolution of the resulting digital image is not 0.5 μm.To achieve true 0.5-μm resolution, the pixelation would need tocorrespond to a region ˜0.2 μm×0.2 μm in the object plane. In onepreferred embodiment, the magnification of the imaging system is set toachieve the true resolution of the optics.

Presently, the highest detection efficiency, lowest noise detectiondevices having sufficient read-out speed for the present applicationsare CCD cameras. In FIG. 11, a rectangular CCD camera is depicted havingan m×n array of detector elements where m is substantially less than n.The image of the fluorescence emission covers one row that is preferablyproximate to the read register. This minimizes transfer time and avoidsaccumulating spurious counts into the signal from the rows between theilluminated row and the read-register.

In principle, one could set the magnification of the optical system sothat the height of the image of the slit SF₂ on the CCD camera is onepixel, as depicted in FIG. 11. In practice, it is difficult to maintainperfect alignment between the illumination line and the camera row-axis,and even more difficult to maintain alignment among three cameras andthe illumination in the multi-wavelength embodiment as exemplified inFIGS. 8 and 9. By binning together a few of the detector elements,exemplarily two to five, in each column of the camera the alignmentcondition can be relaxed while suffering a minimal penalty in read-noiseor read-time.

An additional advantage of the preferred embodiment having one or morerectangular CCD cameras as detection devices in conjunction with avariable-width detection spatial filter, SF₂ in FIGS. 8 and 9 and 510 inFIG. 6, each disposed in a plane conjugate to the object plane, iselucidated by the following. As discussed above, in one embodiment ofthe present invention the detection spatial filter is omitted and aline-camera is used as a combined detection spatial filter and detectiondevice. But as was also discussed above, a variable-width detectionspatial filter permits the optimization of the detection volume so as tooptimize the sample-dependent signal-to-noise ratio. The followingpreferred embodiment retains the advantage of a line-camera, namelyspeed, and the flexibility of a variable detection volume. Themagnification is set so as to image a diffraction-limited line of heighth onto one row of the camera. The width of the detection spatial filterd is preferably variable h≦d≦10 h. The detectors in the illuminatedcolumns of the camera are binned, prior to reading, which is anoperation that requires a negligible time compared to the exposure- andread-times.

In one preferred embodiment, the cameras are Princeton InstrumentsNTE/CCD-1340/100-EMD. The read-rate in a preferred embodiment is 1 MHzat a few electrons of read-noise. The pixel format is 1340×100, and thecamera can be wired to shift the majority of the rows (80%) away fromthe region of interest, making the camera effectively 1340×20.

In addition to the above mentioned advantage of a continuous readcamera, namely the absence of dead-time between successive acquisitions,an additional advantage is that it permits the acquisition ofrectangular images having a length limited only by the extent of thesample. The length is determined by the lesser of the camera width andthe extent of the line illumination. In a preferred embodiment thesample is disposed on the bottom of a well in a 96-well microtiterplate, the diameter of which is 7 mm. A strip 1 μm×1 mm is illuminatedand the radiation emitted from the illuminated area is imaged onto thedetection device. The optical train is designed such that thefield-of-view is ˜1 mm². According to the present invention, an image ofthe well-bottom can be generated at 1-μm pixelation over a 1×7-mm field.

Environmental Control

In an embodiment of the present invention, assays are performed on livecells. Live-cell assays frequently require a reasonable approximation tophysiological conditions to run properly. Among the important parametersis temperature. It is desirable to incorporate a means to raise andlower the temperature, in particular, to maintain the temperature of thesample at 37C. In another embodiment, control over relative humidity,and/or CO₂ and/or O₂ is necessary to maintain the viability of livecells. In addition, controlling humidity to minimize evaporation isimportant for small sample volumes.

Three embodiments providing a microtiter plate at an elevatedtemperature, preferably 37 C, compatible with the LCI system follow.

The imaging system preferably resides within a light-proof enclosure. Ina first embodiment, the sample plate is maintained at the desiredtemperature by maintaining the entire interior of the enclosure at thattemperature. At 37 C, however, unless elevated humidity is purposefullymaintained, evaporation cooling will reduce the sample volume limitingthe assay duration.

A second embodiment provides a heated cover for the microwell platewhich allows the plate to move under the stationary cover. The cover hasa single opening above the well aligned with the optical axis of themicroscope. This opening permits dispensing into the active well whilemaintaining heating and limited circulation to the remainder of theplate. A space between the heated cover plate and microwell plate ofapproximately 0.5 mm allows free movement of the microwell plate andminimizes evaporation. As the contents of the interrogated well areexposed to ambient conditions though the dispenser opening for at most afew seconds, said contents suffer no significant temperature changeduring the measurement.

In a third embodiment, a thin, heated sapphire window is used as a platebottom enclosure. A pattern of resistive heaters along the wellseparators maintain the window temperature at the desired level.

In additional embodiments, the three disclosed methods can be variouslycombined.

Integrated Dispenser

One embodiment of the video-rate configuration of the imaging system isfurther configured to initiate kinetic assays, in particular ion-channelassays, with a timed reagent dispense. Initiation of channel opening isaccomplished by dispensing a solution into the micro well. For example,voltage-gated channels can be opened by addition of a solution of KCl todepolarize the plasma membrane. The time-dependence of the channelopening and subsequent closing and the corresponding change inintracellular concentration is often sufficiently rapid to requirevideo-rate imaging. The intrinsic speed of the imaging system isirrelevant, however, unless the channel response can be initiatedrapidly.

One embodiment of the present invention provides an integrateddispenser. For assays run in 96- or 384-well plates, addition volumes inthis range 20-100 μL are desirable. A single head dispenser, as isappropriate, for example, to the addition of an agonist of ion-channelactivity, is the IVEK Dispense 2000. Comparable units are available fromCAVRO. More generally, it is desirable to be able to dispense a uniquecompound into each well. One embodiment provides a single head dispenseron a robotic motion device that shuttles the dispense head between theanalysis station, the source plate containing the unique compounds andthe tip cleansing station. The latter is a wash station for a fixed tipdispenser and a tip changing station for a disposable tip dispenser.This system provides the desired functionality relatively inexpensively,but it is low throughput, requiring approximately 30 seconds percompound aspiration-dispense-cleanse cycle. An alternative embodiment isprovided by integrating a multi-head dispenser such as the HamiltonMicrolab MPH-96 into the disclosed LCI system. The MPH-96 consists of 96independent fixed tip dispensers mounted to a robotic motion devicecapable of executing the aspirate-dispense-wash cycle described above.

In an additional preferred embodiment of the invention, employed inautomated screening assays, the imaging system is integrated withplate-handling robots, such as the Zymark Twister.

Dark Field Confocal Configuration

In the case that the desired lateral resolution is less than thediffraction limit, the background fluorescence due to the supernatantliquid can be decreased by an inventive application of the dark-fieldimaging technique. FIGS. 12A and 12B depict the ray paths inconventional dark-field. In FIG. 12A, a sample 600 is illuminated by ahollow cone of light 610 from an objective lens 620. This cone of lightis created, for example, by placing an opaque bar 630 at lens 440 inFIG. 10A. In FIG. 12B, the fluorescent emission from sample 600 is thencollected through the center of the objective lens 620. Because of thediffering angles of illumination and collection, the only plane which isboth illuminated and detected is the plane containing sample 600.

FIGS. 13A and 13B depict the ray paths in inverted dark-field. In FIG.13A, a sample 700 is illuminated with a beam of light 710 that passesthrough the center of an objective lens 720. In FIG. 13B, fluorescentemissions are then collected only from around the outside of objectivelens 720. Collection from around the outside of the objective may beachieved by placing, for example, an opaque bar 730 at lens 490 in FIG.10A. Like conventional dark-field, inverted dark-field involvesillumination at one angle and collection at a different angle so thatonly the sample plane is both illuminated and detected.

FIG. 14 depicts the focal region in the case described above where it isadvantageous to illuminate a larger than diffraction-limited area of thesample plane. The illumination and collection rays are the same as thosein the inverted dark-field geometry of FIG. 13. If a stop is placed in aplane conjugate to the objective back focal plane having a width matchedto the illumination beam, the dark-field configuration is achieved. Thatthis configuration confers a decrease in the out-of-plane fluorescenceimpinging on the detector can be understood from FIG. 14. Thefluorescence from the shaded regions above and below the object plane isnot passed by the stop. In point-scan confocal, fluorescence from theseout-of-plane regions is rejected efficiently by the detection aperture.In line-scan confocal, the out-of-plane fluorescence from one lateralposition along the line contributes to the background signal at otherpoints along the line: this is the origin of the degradation insignal-to-background in line-scan relative to point-scan confocal. Theinverse dark-field configuration of line-scan confocal recovers asignificant fraction of the background rejection attributes ofpoint-scan confocal while retaining the speed advantage of the line-scanconfiguration.

Real-Time Data Analysis

The present invention is capable of generating megabytes of data persecond, continuously. In one embodiment, the system is integrated with afast high-density, high-volume storage device to which the data can bespooled in real time for subsequent analysis. In a preferred embodiment,data analysis is run essentially simultaneously with data acquisition.Thus, the data is processed prior to storage. In general, only theresults of the analysis are archived, but it is advantageous to archiveselected raw data, as well.

Examples of real time analysis routines are provided below inconjunction with each of the assay groups. In all cases, procedures areused to optimize the software code for operation on the hardwareplatform of interest. In a presently preferred embodiment, the computeris a 32-bit processor such as the Pentium II. In this case, all data isaccessed in 32-bit parcels.

In general the acquisition and analysis of the data comprises a numberof discrete steps. First, the fluorescence is converted into one or moredigital images in which the digital values are proportional to theintensity of the fluorescent radiation incident on each pixel of thedetection device. Within this step a correction is made for thenon-uniform response of the imaging system across the field of viewwherein the background subtracted data are divided by a so-calledflat-field file. Second, a binary bitmap is generated from one of thedigital images in which all values meeting certain criteria are replacedby one, all values failing to meet the criteria are replaced by zero. Inone embodiment, the criteria include a threshold value determined fromthe image itself. Third, the bitmap is searched for groups of contiguousvalue-one pixels. In one embodiment the groups are further testedagainst minimum- and/or maximum-size criteria. Fourth, for the qualifiedgroups, the values of the corresponding pixels in the same image or inanother image are summed and recorded, and the average and otherstatistical properties of the sums determined and recorded.

Significant throughput gains in digital image processing can be achievedby selecting data representations and algorithms that exploit thehardware architectures and performance behaviors of modern computers. Itis particularly desirable to minimize the time spent accessing mainmemory, to match the data fetching patterns for which high speed cachesare optimized and to use the fastest instructions a given CPU makesavailable: usually those of the integer arithmetic and logic units(ALUs). This can be done by choosing the most compact data format thatadequately encodes the relevant information, addressing the datasequentially whenever possible and selecting algorithms that lendthemselves to parallel computation.

Morphological and spatial measurements such as object shape, size,orientation, location, number and so on are well suited to theseoptimizations because such quantities depend only upon the positions ofpixels in the image rather than the intensities of pixels. Therefore, aone bit per pixel encoding is the preferred data storage format whenstudying these image features. For clarity, the term “image” is used torefer to formats having more than one bit per pixel and the term“bitmap” is used to refer to formats having a single bit per pixel.

While bitmaps (which are one form of spatially defined data) can beused, per se, for the efficient extraction of morphological and spatialinformation, they also serve an equally valuable role in studying theluminosity and density characteristics of objects in the images fromwhich the bitmaps are derived. They do so by serving as masks for theircorresponding images. However, there are more and less efficient meansof applying masks. One technique involves using a mask to alter (writeto) the pixels in the original image. The preferred method assignsread-only status to the original images. The ones and zeros in the maskmerely indicate which pixels of the corresponding image should andshould not be accessed. In a sense, the mask could be viewed as maskingpixel storage addresses rather than pixel data.

For example, suppose one wishes to derive the total intensity of aparticular target object within an image that contains one or more otherobjects in addition to the target as well as background. The recommendedprocedure would be to create a bitmap from the image whose bits B(i,j)are in one-to-one correspondence with the pixels P(i,j) of the image.Next, working exclusively within the bitmap, one would perform whateverbitmap operations are necessary to isolate the target, describing itslocation in both bitmap and image as the set of bits {B(i,j)}. We termsuch sets of related bits “masks.” Finally, to sum the intensities ofthe pixels belonging to the target, one reads and accumulates only thosepixels in the original image corresponding to the {B(i,j)}.

Before applying the bitmap manipulation techniques to be described here,it is necessary to transform the image obtained from the imaging deviceinto the bitmap format. Because no object information is known a priori,it is necessary to scan each pixel in the image and apply some criteriato decide whether the corresponding bit in the bitmap should be set to aone or a zero. The specific criteria to be applied will depend upon theapplication. However, some performance considerations preferably apply:(1) the image should be scanned in sequential order, that is, pixelsshould be scanned and evaluated in the order in which they are stored inmemory; (2) the fastest possible evaluation will comprise the fewestpossible criteria—in particular, one can do no better than having asingle threshold value against which each image pixel is compared; and(3) best performance is achieved if criteria are chosen such that eachbit B(i,j) in the bitmap is derived solely from pixels P(i,j) of theimage, and is not dependent in any way upon values previously calculatedfor other of the B(i,j). This last consideration is especially usefulfor implementing the transformation efficiently in a multiprocessingenvironment. The work can be cleanly segmented among multiple processorsif the results of each are independent.

In accordance with the present invention another technique may also beused. One purpose of this technique is to identify all bits {B(i,j)} ina bitmap that belong to a given object. For clarity, assume that onesrepresent bits within objects and zeroes represent bits in thebackground. The routine requires as input a seed point: a coordinatepair (i,j) (which is one example of a spatial definition) identifying atleast one bit (whose value is one) lying within the target object or onits boundary. This seed point may be found by trial and error byattempting to build an object for each bit having a value of one. Onexit, the routine will have zeroed those bits within the input bitmapthat belong to the object, without having affected any bits notbelonging to the object. In addition, the routine may be made tocalculate other subsidiary spatial information, such as the coordinatesof a bounding box that just encloses the object found, a count of thebits within the object (its area), the centroid of the object ornumerous other results that derive from the fact that each bit belongingto the object will have been examined by the basic algorithm.

The sense of “belonging to” an object is defined recursively as follows:a given bit B(i,j) belongs to an object if it is a one and if any of itsfour nearest neighbors (those immediately above, below, left or right ofthe given bit) has previously been determined to belong to the object.

The algorithm uses a stack (LIFO) data structure, wherein each elementstores the coordinates (i,j) of a bit that has been determined to belongto the object. I.e., as successive object bits are located, theircoordinates are pushed onto the stack. At the start of the routine, thestack is initialized to have exactly one element: the coordinates of theinitial seed point.

The other essential feature of the algorithm is a loop that runs untilall elements of the stack have been popped off, leaving the stackcompletely empty. On each iteration of the loop, the followingoperations are performed:

-   -   (1) The topmost element of the stack is popped off to retrieve        the coordinates of bit B(i,j).    -   (2) Each of the four nearest neighbors of bit B(i,j) is examined        in turn:        -   (a) If the neighbor bit is a zero, it is skipped.        -   (b) If the bit is a one, it fulfills the requirements of an            object bit, so the neighbor's coordinates are pushed onto            the stack.    -   (3) Execution returns to step (1) if the stack is nonempty.

As stated, the basic algorithm outlined here provides a simple frameworkto which can be added other very useful spatial calculations. Forexample, to count the bits in an object, one need only increment acounter variable each time an element is popped off the stack. Asanother example, the coordinates of each element popped off the stackcan be compared to a record of the maximum and minimum position valuesof the bits found so far. In this way, the linear extent of the object(bounding box) can be determined.

After having operated on a bitmap with the above procedure, all the bitsin the target object will have been set to zeroes. If the area, boundingbox or other subsidiary result had been all that was required from thecalculation, the algorithm would be done at this point. However, if amask set {B(i,j)} of object bits is required, then the followingprocedure is recommended. Before executing the object finding routine onan input bitmap (U), a copy of the input bitmap (V) should be set aside.After executing the routine on bitmap (U), it is exactly identical tobitmap (V) except that the target bits have been obliterated in (U). Thefollowing operation will create a new bitmap whose only contents are thedesired {B(i,j)} of the target object:

{B(i,j)}=U XOR V, where XOR is the logical exclusive OR operation.

This may be applied to the entirety of the bitmaps (U) and (V), or forgreater speed, may be applied only to those bits of (U) and (V) withinthe bounding box of the object, found by the method outlined above.

Erosion is the process of excluding pixels from the boundaries ofobjects. The operation is widely used for purposes of separatingadjacent or overlapping objects. The method described makes good use ofmany of the optimization principles mentioned above and lends itselfvery well to multiprocessing environments.

As above, suppose that the bits belonging to an object in the bitmap areencoded as ones, while those bits that do not belong to an object areencoded as zeros. A given bit will be considered to be the boundarypoint of an object if the bit is itself a one and one or more of thefour nearest-neighbor bits (those immediately above, below, left orright of the given bit) is a zero. Such boundary bits should be set tozero by the erosion process. Bits within the interior of an object arethemselves ones and are surrounded by four other ones. These bits shouldremain ones in the eroded bitmap. Any bits that are zero in the originalbitmap should be zero in the eroded bitmap.

Let the bits in the original bitmap be denoted B(i,j) and thecorresponding bits in the eroded bitmap be denoted b(i,j). The erosionrules just stated may be expressed as:

b(i,j)=B(i−1,j)AND B(i,j)AND B(i+1,j)AND B(i,j−1)AND B(i,j+1).

Alternatively, an expression of the rules can be given in terms ofbitmap rows. Let R(i) represent row i of the original bitmap, r(i), thecorresponding row of the eroded bitmap and {R(i)<<, R(i)>>} representthe shifting of row i by one bit to the left and right, respectively.The row-wise expression of erosion then becomes:

r(i)=R(i)<<AND R(i)AND R(i)>>AND R(i−b 1)AND R(i+1).

Very high throughput can be achieved by use of computing machinery thatincludes an N-bit wide ALU, wherein N of the b(i,j) may be computedsimultaneously. Note too, that because the b(i,j) depend only upon theB(i,j), several rows of b(i,j) can be computed in parallel by assigninga range of rows to each of several concurrently operating processors.

Dilation is the process of enlarging objects by advancing theirboundaries outward, into the space currently occupied by background.Using the notations and conventions described previously for bitmaperosion, the process of dilation may be expressed in terms of thefollowing rules. Any bit whose value is one is either an interior pointor a boundary point of an object. The corresponding bit in the dilatedmap should also be one. If a bit has value zero, and one or more of itseight nearest-neighbors is a one, then the bit is exterior to, andimmediately adjacent to an object. Such bits should be set to one in thedilated map. These rules may be stated as bit operations as follows:

b(i, j) = B(i − 1, j − 1)  OR  B(i, j − 1)  OR  B(i + 1, j − 1)  OR  B(i − 1, j)  OR  B(i, j)  OR  B(i + 1, j)  OR  B(i − 1, j + 1)  OR  B(i, j + 1)  OR  B(i + 1, j + 1).

The row-wise expression of the computation is:

r(i) = R(i − 1)<< OR  R(i − 1)  OR  R(i − 1)>> OR  R(i)<< OR  R(i)  OR  R(i)>> OR  R(i + 1)<< OR  R(i + 1)  OR  R(i + 1)>> .

As with erosion, the row-wise algorithm affords the possibility of manysimultaneous calculations of the b(i,j) and can easily be adapted to amultiprocessing environment simply by assigning each processor its ownrange of r(i) to calculate.

Additions to and variations on the basic procedures appropriate to thevarious assays are disclosed below.

Assays

Numerous variations of the assay methods described below can bepracticed in accordance with the invention. In general, a characteristicspatial and/or temporal distribution of one or morefluorescently-labeled species is used to quantify the assay.Advantageously, the fluorescence is observed from an essentially planarsurface using a line-scan confocal microscope. This section is organizedby assay-type according generally to increasing degree of complexity inthe associated data analysis routine. The organization is not strict,however, because the analysis algorithms are often applicable to morethan one assay-type.

Binding Assays

A first assay-type that can be advantageously performed according to themethods of the present invention is a binding assay. In general, thedegree of binding of a fluorescently-labeled ligand to the target ofinterest is quantified from the analysis of one or more fluorescenceimages of a sample containing at least the target and the labeled ligandand obtained with the disclosed line-scan confocal imaging system. Theligands utilized include, but are not limited to, fluorophore conjugatednatural and synthetic peptides and proteins, sugars, lipids, nucleicacid sequences, viral particles, bacteriophage particles, natural andsynthetic toxins, known pharmaceutical agents, small organic moleculesor synthetic analogues of neuro-transmitters or intrinsicallyfluorescent small molecules, peptides or proteins, synthetic compoundsfrom combinatorial libraries, random peptides, proteins from cDNAexpression libraries, and peptidomimetics. (See Haugland R. P. Handbookof Fluorescent Probes and Research Chemicals 6^(th) Ed. Chap. 18.) Thetargets include, but are not limited to cellular extracts or purifiedpreparations of receptors, ligand-gated and ion-gated channel proteins,enzymes, transcription factors, cytoskeletal proteins, and antibodiesand can be derived from viruses, bacteria, bacteriophages, invertebrateand vertebrate cells. Exemplary receptors include but are not limited toacetylcholine, adrenergic (α and β), muscarinic, dopamine, glycine,glutamine, serotonin, aspartate, gamma-amino butyric acid (GABA),purinergic, histamine, norepinephrine, Substance P, Neuropeptide Y,enkephaline, neurotensin, cholecystokinin (CCK), endorphin (opiod),melanocrotin/ACTH, somatostatin, parathyroid hormone, growth hormone,thyrotropin, thyroxin, cytokine, chemokine, insulin, insulin-like growthfactor (IGF), stem cell factor, Luteinizing hormone-releasing hormone,gonadotropin, angiotensin, endothelin, neurotensin, interferon,brakykinin, vasopressin, oxytocin, vasoactive intestinal polypeptide(VIP), corticotropin releasing-hormone, neurotrophin, erythropoetin,prostaglandin, leukotriene, thromboxane A2, calcitonin, T-cell, LDL/HDL,Epidermal growth factor (EGF), Estrogen, and Galainan.

Bead-Based Binding

FIGS. 15A-15F depict the steps of an embodiment of a receptor-bindingassay that can be performed according to the present invention. In FIG.15A, membranes 210 prepared from cells or tissues and containing thereceptor target 212 are added to a well 220 containing a liquid 230. InFIG. 15B, fluorescent-labeled ligands 214 are added to well 220; theseligands bind to the membrane receptors 212. In FIG. 15C, beads 224 areadded to the well 220. Alternatively, the order of 15B and 15C may beinterchanged, and in a preferred embodiment, the membrane-coated beadsare prepared separately, prior to addition to the well.

Beads 224 have a diameter in the range of approximately 1-20 μm and arecoated with a material, such as wheat germ agglutinin, to which themembranes 210 adhere or have a surface that allows for the directcovalent or non-covalent binding of membranes.

The foregoing steps are the same as those of the corresponding steps inthe prior art SSA depicted in FIGS. 1A-1F except that the labels arefluorescent rather than radioactive. However, in the present invention,beads 224 are not luminescent and they have a density such that theysink to, or can be spun down to, the bottom of the well or are magneticso that they can be moved to the bottom of the well using an externalmagnet. In FIG. 15D, the fluorescent labels are imaged using, forexample, a line-scan confocal microscope schematically depicted aselement 240. In FIG. 15E, a test compound 218 is added to the well. Asin the prior art assays, the purpose of the present assay is todetermine the extent to which the test compound displaces thefluorescently-labeled ligands 214 from the membrane receptors 212. InFIG. 15F, the fluorescent labels still bound to the membranes 210 areimaged. By comparing the two fluorescent images, the activity of thetest compound can be determined.

In an alternative embodiment of the assay depicted in FIGS. 15A-15F, theimaging step depicted in FIG. 15D can be eliminated and the activity ofthe test compound can be determined by comparing the image obtained inFIG. 15F to the image of a control well or the image expected from theknown quantity of the fluorescent-labeled ligands added to the well andtheir known affinity to the receptors.

In a specific embodiment of the assay depicted in FIGS. 15A-15F, thereceptor is an antibody that recognizes the ligand, and thefluorescently-labeled ligand is added to the reaction along with asample containing an unknown amount of unlabelled ligand. As in priorart radioimmunoassays, the purpose of the present assay is to determinethe concentration of unlabelled ligand in the sample by measuring extentto which it displaces the fluorescently-labeled ligands 214 from theantibody receptor.

Surface Binding

FIGS. 16A-16F depict the steps of a second embodiment of areceptor-binding assay according to the present invention. In FIG. 16A,membranes 250 prepared from cells or tissues and containing the receptortarget 252 are added to a well 260 containing a liquid 270. The wellbottom 262 is coated with a material such as wheat germ agglutinin, towhich the membranes adhere. In FIG. 16B, membranes 250 are shown boundto this material. In FIG. 16C, fluorescently-labeled ligands 254 areadded to well 260 and bind to the membrane receptors 252. Alternatively,the order of FIGS. 16B and 16C may be interchanged.

In FIG. 16D, the fluorescence of the fluorescent labels is imaged using,for example, a line-scan confocal microscope schematically depicted byelement 280. In FIG. 16E, a test compound 258 is added to well 260. InFIG. 16F, the fluorescent labels still attached to the membranes 250 areimaged and compared to the first image to determine the activity of testcompound 258.

In an alternative embodiment of the assay depicted in FIGS. 16A-16F, theimaging in FIG. 16D can be eliminated and the activity of the testcompound can be determined by comparing the image obtained in FIG. 16Fto the image of a control well or the image expected from the knownquantity of the fluorescent-labeled ligands added to the well and theirknown affinity to the receptors.

Cell-Based Binding

In an alternative embodiment, ligand-target binding is advantageouslyassayed on collections of cells expressing the target. In general, thereare a number of advantages to cell-based assays for screening chemicalcompounds. In particular, the activity of interest is measured in thepresence of both competing and complementary cellular processesaffecting the biological activity of the compound. In cellular assays,cells prepared from cell lines or tissues are placed in tissue culturewells or on microscope slides. The cells can be live and intact orpermeabilized with reagents such as digoxigenin, or, alternatively,fixed with reagents such as formaldehyde. One or morefluorescent-labelled ligands are added to the cells along with anynon-fluorescent reagents required for the assay; thefluorescent-labelled ligands bind to one or more components of thecells. A test compound is then added to the cells. Alternatively, theorder of addition of fluorescent ligands and chemical compounds may beinterchanged. The fluorescent labels are imaged using, for example, aline-scan confocal microscope schematically depicted as element 240. Thepurpose of the present assay is to determine the extent to which thetest compound displaces the fluorescently-labeled ligands from thereceptors. The fluorescent labels still bound to the cells are imaged inthe presence and the absence of test compound. By comparing the twofluorescent images, the activity of the test compound can be determined.

In an alternative embodiment of a cell-based receptor binding assay, theimaging step in the absence of compound can be eliminated and theactivity of the test compound can be determined by comparing the imageobtained in the presence of compound to the image of a control well orthe image expected from the known quantity of the fluorescent-labeledligands added to the well and their known affinity to the receptors.

Advantages of Linescan Confocal Imaging in Binding Assays

In a first embodiment, ligand-target binding is performed with oneexcitation wavelength and one emission wavelength. Data are provided inFIG. 27 exemplifying the speed and sensitivity of the present invention.A detailed analysis of its performance relative to the prior art whereinligands are radiolabeled to allow for their detection, follows. Theprior art for receptor-ligand assays includes SSA formats as well asformats in which bound and unbound ligand are physically separated andthe amount of ligand bound to the receptor is measured by the additionof liquid scintillant.

First, the present invention can be used in small-volume wells,exemplarily I μL. In a receptor-ligand binding assay employingradiolabeled ligand, each radio label, ³H for example, can decay onlyonce, producing at most 90 photons per decay, at a decay rate of lessthan 10⁻⁸ per second. A single fluorescent molecule, will produce 10⁴-10⁷ photons in total, and it will emit between 10³ and 10⁶ photons persecond. Thus, the count-rate for a fluorescent label is approximately10³ relative to ³H. The present invention, therefore, requires immenselyfewer labels, membranes and beads per well. For example, while a tritiumSSA requires 10⁷ beads per well, the present invention requires lessthan 10³ beads per well. As a result, the present invention can beperformed in μL-volume wells and in far less time. In addition, in anSSA it is difficult to alter the imaging time, because radio labelsdecay at a fixed rate. In contrast, the excitation rate of fluorescentlabels can be increased so as to increase the photon emission rate,thereby reducing the required imaging time. The excitation rate cannot,however, be increased without limit. In fact, it is the existence of theso-called saturation limit of the fluorophore emission rate thatunderlies the substantial advantage of the line-scan confocal over thepoint-scan confocal in the present application. Second, the presentinvention does not require the time and expense of handlingradioactivity. Third, because the present invention can be performed insmall-volume wells, the compound and reagent consumption is much lowerthan for SSAs resulting in further cost reductions. Finally, the presentinvention does not require scintillant-doped beads or well bottoms,reducing costs even further.

The present invention uses a line-scan confocal microscope to image thefluorescence of the sample in the well. The confocal aspect of themicroscope allows for optical sectioning, i.e., detection offluorescence from the plane in which the sample is located whileminimizing the detection of fluorescence from the bulk of the solution.This eliminates the need for wash steps to remove unboundfluorescent-labeled ligand; this step, while it is not required in anSSA, is still required in any receptor-ligand binding assay, includingRIA, in which scintillant containing beads are not used. The confocalaspect of the microscope also eliminates any interference that mayoriginate from intrinsic fluorescent test compounds. The line-scanaspect allows the sample to be imaged more rapidly than in traditionalpoint-scanning without losing appreciable background rejection. Thespeed increase depends on the fluorophore density, the lateralresolution, the field of view, and parameters of the hardware includingthe objective NA, the detection sensitivity and camera read-rate.Theoretically, the speed increase can approach the number of pixels perline, which is 1000 in a preferred embodiment of the present invention.Practically, the increase is approximately 100×.

In order to quantify these advantages, an exemplary sample will bedescribed. The assay is cell-based, wherein the location of thefluorescence is to be resolved to a precision of 1 μm. Thus the image ofa 1-mm diameter sample area will consist of ˜10³ lines of ˜10³ pixels.The fluorescence signal of interest might originate from ligands on thecell surface or from a localized source within the cell, such as areceptor in the nucleus. In either case, the local concentration of thefluorophore is the important parameter. For an engineered cell lineexpressing ˜10⁵ receptors per cell, the cell-averaged concentration is˜1 μM. A few thousand receptors localized in the nucleus results in acomparable local concentration. Consistent with the desired lateralresolution of ˜1 μm, there are ˜2×10³ fluorophores per pixel. It isassumed that the intrinsic cellular background fluorescence is lessthan, but on the order of, the label fluorescence, and that the desiredsignal-to-noise ratio is minimally 10. Then, the number of detectedphotons needs to be nearly 10³, taking into account the shot noise ofthe signal and background and the read noise of a high quality solidstate detector. The collection and detection efficiency of the presentdevice, using an approximately 0.7 NA objective, blocking filters, and asolid state camera is ˜1%, requiring that ˜10⁵ photons be emitted perpixel, or ˜10² photons per molecule. It is desirable that the image beacquired in less than 1 second, preferably in a fraction of a second. Ifthe pixels are acquired in a serial fashion, then the pixel dwell-timemust be less than 1 μs, requiring a photon emission rate of greater than10⁸ per second per molecule. This is beyond the saturation value of mostfluorophores, which is typically 10⁶. Importantly, the flux required toachieve saturation, 10⁵-10 ⁶ W/cm², is sufficient to drive non-linearphoto-induced bleaching of the fluorophores, as well. Finally, thehighest efficiency detection devices cannot be used at the data ratesrequired in serial scanning. By contrast, the emission rate perfluorophore need only be ˜10⁵ if 10³ pixels are illuminatedsimultaneously. The increased rejection of background fluorescence ofpoint-scan confocal does not warrant the disadvantage of dramaticallydecreased scan speed.

The exemplary data of FIG. 27 demonstrate that the disclosed system hassufficient sensitivity to quantify tens of fluorophores per bead, whileclearly resolving hundreds of individual beads in less than 1 second.Comparable data can be acquired in cell-based binding experiments, aswill be exemplified below.

Data Analysis

The data analysis routines are closely related whether the binding becell-based or bead-based and are presented together, below. The data canbe analyzed by the following routines, the simplest of which is theThreshold Image Analysis algorithm. The purpose of the routine is todetermine the amount of a fluorescently-labeled species that islocalized in a contiguous or punctuate manner so as to exceed a minimumfluorescence intensity, and optionally so as to not exceed a maximumfluorescence intensity. In one embodiment the analysis is used to assaythe activity of a chemical compound.

The steps of the algorithm are as follows:

-   -   1. Acquire a digitized image of the labeled species.    -   2. Open file row-by-row and        -   i. Subtract camera offset value from image,        -   ii. Multiply each row in the image by the inverse of the            corresponding row in the flat-field image file.    -   3. Optionally, histogram the image to determine the background        level.    -   4. Establish selection criteria including a minimum value and        optionally a maximum value. The values are determined, for        example, as a fixed multiple of the mean background level, as a        fixed number of counts above the mean background level, by        statistical analysis on the background histogram peak width or        by using a pre-determined value.    -   5. Compare each pixel in the image to the selection criteria.        For each pixel in the image meeting the criteria, add the value        to a running sum. The total number of qualified pixels and the        average intensity are reported.

This routine is used advantageously to process data similar to that inFIG. 27, in which the individual beads are clearly distinguishable fromthe background and the artifacts due to clumped beads or cells aresmall. Such a routine is appropriate for the assay-type having membranesbound to the well bottom, as well.

A second routine applicable to analyzing binding data is theLocalization Analysis algorithm which entails an additional shapeanalysis protocol. As with the Threshold routine, the purpose is todetermine the amount of a fluorescently-labeled species that islocalized in a contiguous or punctuate manner. In one embodiment theanalysis is used to assay the activity of a chemical compound.

The steps of the algorithm are as follows:

-   -   1. Acquire image of the labeled species.    -   2. Open file row-by-row and        -   i. Subtract camera offset value from the image,        -   ii. Multiply each row in the image by the inverse of the            corresponding row in the flat-field image file.    -   3. Optionally, histogram and sum the pixel values of the image.    -   4. Establish selection criteria including a minimum value and        optionally a maximum value. The values are determined, for        example, as a fixed multiple of the mean background level, as a        fixed number of counts above the mean background level, by        statistical analysis on the background histogram peak width or        by using a pre-determined value.    -   5. Compare each pixel in the image to the selection criteria.        All qualified pixels are assigned a value of 1 and all others        are assigned a value of 0, thereby effecting a 16- to 1-bit        compression.    -   6. “Clean” the edge of the image by setting to 0 all 1-valued        contiguous pixels in the binary mask having an edge-touching        member.    -   7. Search the bitmap for objects, defined as groups of        contiguous value-1 pixels, by:        -   i Searching the image in a line-by-line pattern to find a            pixel of value 1.        -   ii Determining all value-1 pixels contiguous to the pixel            identified in i).        -   iii Optionally, applying a minimum and maximum size filter            to the object, the sizes having been previously determined.        -   iv If the object qualifies, proceed to step 8, otherwise            change all 1-valued pixels in the object to 0 and continue            searching for next object.        -   v If the end of the bitmap is reached, proceed to step 9.    -   8. For each object passing the filter criteria:        -   i Optionally, create a new rectangular bitmap with extended            borders that contains the object plus n extra 0 pixels in            each direction from the edge of the object. n is the number            of dilation steps to be performed below and has been            previously determined.        -   ii If step 8.i. was implemented, then dilate the object by            applying a dilation step n times in which pixels of value 0            that touch 1-valued pixels are set to value 1.        -   iii For each collection of 1-valued pixels in either the            dilated bitmap, or in the original bitmap if step 8.i. was            not implemented, sum and average the corresponding pixel            values from the image to calculate the average pixel            intensities under the mask.        -   iv Change to 0 all pixels of the object in the original            bitmap image and return to step 7 to search for more            objects.    -   9. After all objects have been counted, the average intensity of        the fluorescently-labeled species per object and optionally the        fraction of the total intensity of the species localized is        calculated for all objects in the image and reported together        with statistical information such as the standard deviation.

The distinguishing operation in this routine, shared by all thefollowing algorithms, is the creation of the binary mask in steps 4-6.Mask generation is depicted in FIG. 20. The selection criteria ofobjects for the mask can optionally include minimum and maximum values,size and shape. For example, in one embodiment, the analysis routine forthe bead-based assays include a roundness filter in step 7.iii.

In a second embodiment, the emission of two or morefluorescently-labeled species is detected simultaneously, excited by oneor more illumination wavelengths. As applied in a binding assay, thefirst fluorescently-labeled species is used to identify the object towhich the second fluorescently-labeled species binds. Two examples oftwo-color cell-based binding assays are provided in FIGS. 24 and 26. Anexemplary procedure that can be used to analyze such images is theCo-localization Analysis routine which is designed to determine theamount of a first fluorescently-labeled species localized with respectto a second fluorescently-labeled species. In one embodiment theanalysis is used to assay the activity of a chemical compound, forexample, where activity depends on a subcellular localization ofinterest.

The steps of the algorithm are as follows:

-   -   1. Acquire digitized images of the first and second labeled        species respectively.    -   2. Open files row-by-row and        -   i. Subtract respective camera offset values from each image,        -   ii. Multiply each row in each image by the inverse of the            corresponding row in its respective flat field image file.    -   3. Optionally, histogram the image of the first species to        determine the background level and sum the intensity of the        image of the second species.    -   4. Establish selection criteria including a minimum value and        optionally a maximum value. These values are determined, for        example, as a fixed multiple of the mean background level, as a        fixed number of counts above the mean background level, by        statistical analysis on the background histogram peak width or        by using a pre-determined value.    -   5. Compare each pixel in the image of the first species to the        selection criteria. All qualified pixels are assigned a value of        1 and all others are assigned a value of 0, thereby effecting a        16- to 1-bit compression.    -   6. “Clean” the edge of the image by setting to 0 all 1-valued        contiguous pixels in the binary mask having an edge-touching        member.    -   7. Search the bitmap for objects, defined as groups of        contiguous value-1 pixels, by:        -   i Searching the image in a line-by-line pattern to find a            pixel of value 1.        -   ii Determining all value-1 pixels, contiguous to the pixel            identified in i).        -   iii Optionally, applying a minimum and maximum size filter            to the object, the sizes having been previously determined.        -   iv If the object qualifies, proceed to step 8, otherwise            change all 1-valued pixels in the object to 0 and continue            searching for next object.        -   v If the end of the bitmap is reached, proceed to step 9.    -   8. For each object passing the filter criteria:        -   i Optionally, create a new rectangular bitmap with extended            borders that contains the object plus n extra 0 pixels in            each direction from the edge of the object. n is the number            of dilation steps to be performed below and has been            previously determined.        -   ii If step 8.i. was implemented, then dilate the object by            applying a dilation step n times in which pixels of value 0            that touch 1-valued pixels are set to value 1.        -   iii For each collection of 1-valued pixels in either the            dilated bitmap, or the original bitmap if step 8.i. was not            executed, sum and average the corresponding pixel values            from the image of the second species to calculate the            average pixel intensities under the mask.        -   iv Change to 0 all pixels of the object in the original            bitmap image and return to step 7 to search for more            objects.    -   9. After all objects have been counted, the average intensity of        the second fluorescently-labeled species per object and        optionally the fraction of the total intensity of the second        species co-localized with the first species is calculated for        all objects in the image and reported together with statistical        information such as the standard deviation.

The advantage of this more elaborate routine is that the object, whetherit be a cell or a bead, can be independently identified. As exemplifiedin FIG. 24, not all cells respond. The independent identification ofcells, enables, for example, the ratio of responding to non-respondingcells to be tabulated along with the degree of response among those thatrespond. This algorithm, despite its additional complexity, can beimplemented so as to analyze 1-Megapixel images in under 1 second on aPentium II platform.

Translocation Assays

An additional assay-type that can be performed advantageously accordingto the second embodiment, that is where the emission of two or morefluorescently-labeled species is detected simultaneously, excited by oneor more illumination wavelengths, is the translocation assay. In theseassays, the translocation of interest is of one or more species, whichmay be proteins, lipids or other molecular complexes or sub-cellularstructures such as vesicles, from one well-defined region of a cell toanother. These include but are not limited to: synaptin (vesiclemembrane protein), transcription factors (NF-κB, NFAT, AP-1), hormonereceptors, LDL/HDL receptors, T-cell receptors, and PTH receptors.

The prototypical translocation assay is a special case of theco-localization measurement. Exemplarily, the co-localization of thefirst and second species is quantified by the fraction of the secondspecies co-localized with respect to the first, or the ratio of thesecond species co-localized with the first and that resident elsewherein the cell. An expanded analysis routine preferentially used to processtranslocation image data is provided below.

Exemplary translocation images and analysis procedures are provided inFIGS. 19-21. The labeled location is the cell nucleus, the label being afluorophore specific for DNA, such as Hoechst 33342. Other nucleic acidspecific stains are known in the art (e.g., see Haugland, R. P. Handbookof Fluorescent Probes and Research Chemicals, 6th Ed. Chapter 8). Thesecond species is a transcription factor whose migration from thecytoplasm to the nucleus is the subject of the assay. This protein canbe labeled by a variety of methods, including expression as a fusionwith GFP, and contacting the sample with a fluorescently-labeledantibody specific to the transcription factor protein.

The following Translocation Data Analysis routine can be used todetermine the amount of a first fluorescently-labeled species that isdistributed in a correlated or anti-correlated manner with respect to asecond fluorescently-labeled species. In one embodiment the analysis isused to assay the activity of a chemical compound.

The steps of the algorithm are as follows:

-   -   1. Acquire images of the first and second labeled species        respectively.    -   2. Open files row-by-row and i. Subtract respective camera        offset values from each image,        -   ii. Multiply each row in each image by the inverse of the            corresponding row in its respective flat-field image file.    -   3. Optionally, histogram the image of the first species to        determine the background level and sum the intensity of the        image of the second species.    -   4. Establish selection criteria including a minimum value and        optionally a maximum value. These values are determined, for        example, as a fixed multiple of the mean background level, as a        fixed number of counts above the mean background level, by        statistical analysis on the background histogram peak width or        by using a pre-determined value.    -   5: Compare each pixel in the image of the first species to the        selection criteria. All qualified pixels are assigned a value of        1 and all others are assigned a value of 0, thereby effecting a        16- to 1-bit compression.    -   6. “Clean” the edge of the image by setting to 0 all 1-valued        contiguous pixels in the binary mask having an edge-touching        member.    -   7. Search the bitmap for objects, defined as groups of        contiguous value-1 pixels, by:        -   i Searching the image in a line-by-line pattern to find a            pixel of value 1.        -   ii Determining all value-1 pixels contiguous to the pixel            identified in i).        -   iii Optionally, applying a minimum and maximum size filter            to the object, the size having been previously determined.        -   iv If the object qualifies, proceed to step 8, otherwise            change all 1-valued pixels in the object to 0 and continue            searching for next object.        -   v If the end of the bitmap is reached, proceed to step 9.    -   8. For each object passing the filter criteria:        -   i Create a new rectangular bitmap with extended borders that            contains the object plus n extra 0 pixels in each direction            from the edge of the object. n is the number of dilation            steps to be performed below and has been previously            determined.        -   ii Dilate the object by applying a dilation step n times in            which pixels of value 0 that touch 1-valued pixels are set            to value 1.        -   iii Compare the dilated bitmap with the original full size            bitmap. Set to 0 all pixels in the dilated bitmap that are            1-valued in the corresponding region of the original bitmap.            This produces an annular mask and ensures only one object is            captured when the bitmap borders were increased during            dilation.        -   iv Create another bitmap from the original object, erode it            m times by setting to 0 value-1 pixels touching value-0            pixels. m is typically equal to n and determined previously.        -   v For each collection of 1-valued pixels in the annular and            eroded bitmaps, average the corresponding pixel values from            the image of the second species to calculate the average            pixel intensities under the eroded and annular masks.        -   vi Calculate the ratio of eroded to annular intensities for            each object and save in a table.        -   vii Change to 0 all pixels of the object in the original            bitmap image and return to step 7 to search for more            objects.    -   9. After all objects have been counted, the average intensity        ratio of all objects in the image is calculated along with        statistical information such as the standard deviation.

The new feature of this routine over those disclosed above is thecreation in Step 8 of two daughter masks, one an annular extension ofthe primary mask, and one an eroded version of the primary mask. Thelatter is used to quantify the co-localization of species-two withspecies-one, the transcription factor and the cell nucleus (actually,DNA), respectively, in the present example. The former mask is used toquantify species-two not co-localized. In the present example, the ratioof these two quantities is formed on an cell-by-cell basis and theresults tabulated.

According to the methods of the present invention, the data acquisitionand analysis can be performed in approximately one second. Forcomparison, two prior art examples are cited. In Ding et al. (J. Biol.Chem., 273, 28897-28905 (1998)), a comparable two-color translocationassay was performed. The advantages of the present invention include: 1)approximately 50× faster image acquisition per data channel, 2)simultaneous two-color image acquisition, 3) superior sensitivity ofapproximately 10×, permitting lower staining levels, 4) confocaldetection, allowing elimination of a rinse step, 5) focus-time ofapproximately 0.1 s compared to approximately 30 s, 6) data analysistime of approximately 0.2 s/frame compared to 3-6 s/frame, and 7)continuous image acquisition. The second example of prior art is Deptalaet al. (Cytometry, 33, 376-382, (1998)). The present inventionprovides 1) higher spatial resolution, approximately 4×, 2)approximately 16× higher pixel acquisition rates, 3) faster dataanalysis, 4) autofocus operable in microtiter plates, and 5) dataanalysis time of approximately 0.2 s/frame compared to 3-6 s/frame.

Endocytosis, Exocytosis and Receptor Sequestration

Endocytosis and exocytosis, generally, and receptor sequestration andrecycling, specifically, are additional processes that can be assayedaccording to the first or second embodiments and the associated imageanalysis protocols disclosed above. Fluorescence labeling can beaccomplished according to a variety of known methods. For example, anelegant experiment comprising the labeling of both the receptor andligand is disclosed by Tarasova et al. (J. Biol. Chem., 272, 14817-14824(1997)). The present imaging system is approximately 50× faster per datachannel and acquires the two images simultaneously. In addition, thepresent analysis protocols, the Co-localization algorithm for example,can be used to process sequestration image data in real-time. No suchexamples are known in the prior art.

Many other assays requiring similar imaging and analysis capabilitiesare known in the art. For example, assays involving phagocytosis andrelated cellular events, (e.g., J. Immunology, (1983) 130, 1910; J.Leukocyte Biol. (1988) 43, 304); additional assays involving bothreceptor-mediated and non-receptor-mediated endocytosis and exocytosis(e.g. Neuron 14, 983 (1995); J. Physiol. 460, 287 (1993) and Science255, 200 (1992), including receptor-mediated endocytosis of Low-DensityLipoprotein Complexes (see J. Cell Biol. 121, 1257 (1993) and thedelivery of Transferin to vertebrate cells (see Cell 49, 423 (1994));imaging the endocytosis and lateral mobility of fluorescently-labeledepidermal growth factor (see Proc. Natl. Acad. Sci. USA 75, 2135 (1975);J. Cell Biol. 109, 2105 (1989)); monitoring the uptake and internalprocessing of exogenous materials by endocytosis of fluorescent dextrans(see J. Biol. Chem. 269, 12918 (1994)), and the imaging of theendocytosis-mediated recycling of synaptic vesicles in actively firingneurons by use of hydrophilic dyes (see Nature 314, 357 (1985)). Inaddition, the genetic engineering of cell lines expressing greenfluorescent protein (GFP)fused to proteins that localize to exocytoticand secretory vesicles (such as chromogranin B, a secretory granuleprotein (see J. Cell Sci. 110,1453 (1997) or tPA which is localized togrowth cones in differentiated neuronal cells (see Mol. Biol. Cell 9:2463 (1998)) allow for the monitoring of exocytosis. A wide variety offluorescent labels are available for such assays (See Haugland R. P.Handbook of Fluorescent Probes and Research chemicals, 6^(th) Ed. Chap.17).

Ion Channels

A third embodiment of the present invention, one version of which isdepicted in FIG. 9, can be used to image the time-dependent response ofone or more fluorescently-labeled species at a rate of approximately 30frames per second. This permits the capture of transient phenomenon,such as the opening and closing of ion channels. Exemplary ion channelsinclude but are not limited to: K⁺-gated voltage, Na⁺-gated voltage,Ca⁺⁺-gated voltage, Cl⁻, Na⁺/K⁺ ATPase, and P-glycoproteins.

The following Kinetic Imaging Data Analysis algorithm defines and tracksindividual cells from frame to frame, enabling simultaneous kineticanalysis on a sufficient number of cells to obtain statisticallymeaningful data.

The steps of the algorithm are as follows:

-   -   1. Acquire one (indicator only), two (marker and indicator or        two indicators) or more digitized images as a function of time.    -   2. Open files row-by-row and        -   i. Subtract respective camera offset values from each image,        -   ii. Multiply each row in each image by the inverse of the            corresponding row in its respective flat-field image file.            Subtract respective camera offset values from each image.    -   3. Optionally, histogram the image of the first species to        determine the background level.    -   4. Establish selection criteria including a minimum value and        optionally a maximum value. The values are determined, for        example, as a fixed multiple of the mean background level, as a        fixed number of counts above the mean background level, by        statistical analysis on the background histogram peak width or        by using a pre-determined value.    -   5. Compare each pixel in the image of the first species to the        selection criteria. All qualified pixels are assigned a value of        1 and all others are assigned a value of 0, thereby effecting a        16- to 1-bit compression.    -   6. “Clean” the edge of the image by setting to 0 all 1-valued        contiguous pixels in the binary mask having an edge-touching        member.    -   7. Search the bitmap for objects, defined as groups of        contiguous value-1 pixels, by:        -   i Searching the image in a line-by-line pattern to find a            pixel of value 1.        -   ii Determining all value-1 pixels contiguous to the pixel            identified in i.        -   iii. Optionally, applying a minimum and maximum size filter            to the object, the size having been previously determined.        -   iv. If the object qualifies, proceed to step 8, otherwise            change to 0 all 1-valued pixels in the object and continue            searching for next object.        -   v. If the end of the bitmap is reached, proceed to step 9.    -   8. For each object passing the filter criteria: average the        corresponding pixels from each of the images in the time series.        If a single indicator is used, record the intensities. If        ratiometric indicators are used, divide the value of one image        by the other for each image in the time series and record the        results.    -   9. After all objects have been analyzed, the results of the        analysis of step 8 are reported for each object. Kinetic        parameters, including the rise time, fall time and amplitude are        reported for each object as are statistical information derived        from the set of kinetic analyses and from the set of all objects        at fixed times.

Two examples of the use of the present invention to image and analyzetransient events associated with ion channels are provided in FIGS. 22and 23. These assays used the Ca⁺⁺-sensitive dye, Fluo-3 to indicate thechanges in intra-cellular Ca⁺⁺ concentration. In the first of theexperiments, the change was caused by aCa^(++ second signal initiated by the activation of acetylcholine receptors, and in the second experiment the change was due to activation of voltage-gated Ca)⁺⁺ channels.

Ion channels have been an area of intense research activity in recentyears. The advantages of the present invention over the prior art willbe made clear by the following comparisons.

In compound screening applications, a prior art standard, cited in theBackground Section, is disclosed in U.S. Pat. No. 5,355,215. Thisdevice, used primarily for detecting induced changes in intracellularCa²⁺, includes a dispenser to initiate transient events. The principaladvantages of the present invention over this prior art are thefollowing: 1) imaging and analysis permitting the determination ofindividual cellular responses as compared to a response averaged overthe well, 2) increased sensitivity, requiring lower reagent loading andlower illumination intensity, and enabling smaller sample volumes, and3) the acquisition of images at video rates compared to a maximum rateof 1 point per second.

In research applications, the system of Tsien and co-workers disclosedin the Handbook of Biological Confocal Microscopy, J. B. Pawley, ed.,Plenum Press, New York, 1995, pp. 459-478, serves as a standard. It hasa demonstrated capability to image at rates beyond the presentinvention. This cannot be accomplished, however, on samples presently ofinterest. The prior art requires 102-103 greater fluorophores per pixelto achieve rates comparable to the present invention at a comparablesignal-to-noise ratio. In addition, the present invention can acquireimages at 12- or 16-bit resolution, giving it a 4-16× greater dynamicrange.

A second example of a research system is disclosed in Sun et al., J.Physiology, 509, 67-80, 1998. According to Sun, data is generated atrates up to 650 Hz per 600-pixel line with 5 microsecond per pixelintegration time, using a conventional spot scanning confocalmicroscope. Only one-dimensional “imaging” is performed. Transients canbe monitored for objects lying along the scanned line. In addition, thisrate could only be achieved with 1-μs pixel integration time, requiringa 10²-10 ³ greater concentration of fluorophores to achieve imagequality comparable to the present invention.

The capabilities of the present invention to image and analyze changesin intra-cellular ion concentrations in response to external stimuli hasmultiple applications in compound screening and in general biologicalresearch applications. (See e.g. J. Cell Biol. 137(3), 633-648 (1997);J. Biol. Chem. 271(9), 4999-5006 (1996); Science 280, 69-76 (1998);Biochem, J., 324, 645-651 (1997)). A wide variety of fluorescentindicators are available sensitive to specific ions (see Haugland R. P.Handbook of Fluorescent Probes and Research Chemicals, 6^(th) Ed. Chaps18, 22 and 24). These indicators allow measurement of concentrations ofMg²⁺, Zn²⁺, Ca²⁺, Na⁺, Fe²⁺ Hg²⁺, Pb²⁺, Cd²⁺, Ni²⁺, Co²⁺ Al³⁺, Ga²⁺,Eu³⁺, Tb³⁺, Tb³⁺, Sm³⁺, and Dy³⁺. In addition, assays for Na⁺ and K⁺ canbe performed even in the presence of physiological concentrations ofother monovalent cations (see J. Biol. Chem. 264, 19449 (1989)),including assays of Na⁺ levels or Na⁺ efflux in a variety of cells suchas blood, brain and muscle cells (see J. biol. Chem. 268, 18640 (1993);J. Neurosci. 14, 2464 (1994); Am J. Physiol. 267, H568 (1994)), andchanges in K⁺ in sperm cells, nerve terminals synaptosomes andlymphocytes. In addition, the present invention can be used to assay Cl⁻concentrations in vesicles, liposomes and live cells (see Am. J.Physiol. 259, c375 (1990).

In addition, the present invention can be used to assay changes inmembrane potential in cells and sub-cellular organelles. The ability torapidly image changes in membrane potential is vital to assays for celland organelle viability, nerve-impulse generation, muscle contraction,cell signaling and ion-channel gating (see Biophys J. 67, 208 (1994);Neuron 13, 1187 (1994); J. Membrane Biol. 130, 1 (1992)). Fluorescentindicators are available that respond to fast (millisecond) potentialchanges in excitable cells such as neurons, cardiac cells and intactbrain cells. (See Haugland R. P. Handbook of Fluorescent probes andResearch Chemicals, 6^(th) Ed. Chap. 25). The fluorescent probes thatrespond to fast transmembrane potential changes typically show only a2-10% change in fluorescence per 100 mv. The plasma membrane of a cellhas a transmembrane potential of approximately −70 mv and someorganelles such as mitochondria maintain transmembrane potentials of−150 mV. Thus, assays involving such rapid changes require the highsensitivity, rapid data acquisition ability common to the variousembodiments of the present invention.

Fret-Based Measurements

The present invention can be advantageously used to perform assays whichinvolve fluorescence resonance energy transfer (FRET). FRET occurs whenone fluorophore, the donor, absorbs a photon and transfers the absorbedenergy non-radioactively to another fluorophore, the acceptor. Theacceptor then emits the energy at its characteristic wavelength. Thedonor and acceptor molecules must be in close proximity, less thanapproximately 10 nm, for efficient energy transfer to occur (see MethodsEnzymol. 211, 353-388 (1992); Methods Enzymol. 246, 300-334 (1995)). Theproximity requirement can be used to construct assays sensitive to smallseparations between the donor-acceptor pair. FRET typically requires asingle excitation wavelength and two emission wavelengths, and ananalysis consisting of the ratio of the donor and acceptor emissionintensities. FRET donor acceptor pairs can be constructed for bothbead-based assays and cell-based assays. Several green fluorescentprotein (GFP) mutants displaying enhanced fluorescence and alteredemission wavelengths can be paired for FRET cell-based assays by fusingthe GFP FRET donor to one protein and the GFP FRET acceptor to eitherthe same protein or to another protein expressed within the same cell.Such FRET pairing can be used to measure intramolecular changes, such asCa²⁺-calmodulin binding of Ca²⁺ or intermolecular interactions, such asreceptor dimerization. The Kinetic Imaging algorithm disclosed above canbe preferentially used.

Transient Transfection

Among the significant advantages of an image-based measurement is theopportunity both to observe rare events, lost within the average, and tonormalize the primary response on an object-by-object basis to asecondary, response. Both features can be important in assays using acell line having a transiently transfected target. Gene expression andsubsequent protein production following transfection is ofteninefficient and transient (see BioTechniques 24:478-482 (1998)). Methodsto monitor the transfection efficiency that can be advantageously usedwith the present invention are known in the art. For example, the geneof interest can be transfected together with the gene for greenfluorescent protein (GFP), so that the two proteins will be expressedeither as a fusion or as separate entities. The present invention can beused to measure the amount of indicator present at one wavelength andthe response associated with the target at another. The former signalcan be used to normalize the response of the latter for the amount oftarget present. This allows the present invention to perform assays ontargets too unstable to be used in currently available screening and tomonitor transfection efficiencies of only a few percent. The KineticImaging algorithm disclosed above can be used to analyze such data,where only one image frame is required. Viral infection of cells can bemonitored, either directly through expression of viral proteins, orindirectly by acquisition of a new phenotype, even if only a few percentof cells are infected. Finally, this invention provides a method fordetecting a rare event, such as the acquisition of a new phenotype by anindividual cell or group of cells due to the transfection of a specificcDNA as a result of the transfection of the entire cell population witha library of diverse cDNAs.

Enzyme Assays

The present invention can also be used to conduct general assays ofenzyme activity. Exemplary intracellular enzymes include but are notlimited to: carbonic anhydrase, guanine nucleotide-binding proteins (Gproteins), adenyl cyclase, calmodulin, PI, PIP and PIP2 kinases, cAMPkinase and cAMP hydrolase, cytochrome P-450, serine/threonine proteinkinases, tyrosine protein kinases, protein phosphatases, β-lactamase,β-galactosidase, dihydrofolate reductase, phosphodiesterases, caspases,proteosome proteases, nitric oxide synthase, thymidine kinase,nucleoside deaminase, glutathione-S-transferase, lipoxygenases, andphospholipases.

FIGS. 17A-17D depict the steps of a first embodiment of an enzyme assayaccording to the present invention. In FIG. 17A, beads 310 with a knownquantity of fluorescent-labeled peptides 312 attached thereto are addedto a well 320 containing a liquid 330. Beads 310 have a density suchthat they sink to the bottom of the well. In FIG. 17B, a test compound314 is added to the well. In FIG. 17C, enzymes 316 are added to thewell. The order of the steps depicted in FIGS. 17A, 17B and 17C isinterchangeable except that at no time should the well contain thepeptides and enzymes without the test compound. If not inhibited,enzymes 316 will cleave peptides 312, and the fluorescent labels willdiffuse into the liquid. If, on the other hand, test compound 314inhibits enzymes 316, typically by blocking the enzyme active sites,enzymes 316 will not cleave the fluorescent labels. In FIG. 17D, thefluorescent labels still attached to the beads are imaged using, forexample, a line-scan confocal microscope schematically depicted aselement 340. From this image, the activity of test compound 314 can bedetermined.

In an alternative embodiment of the assay depicted in FIGS. 17A-17D, theactivity of the test compound can be determined by comparing the imageobtained in FIG. 17D to the image obtained by imaging the fluorescenceof the fluorescent labels in FIG. 17A or 17B or the image of a controlwell.

FIGS. 18A-18D depict the steps of a second embodiment of an enzyme assayaccording to the present invention. In FIG. 18A, a known quantity offluorescent-labeled peptides 352 are attached to the bottom 362 of awell 360. In FIG. 18B, a test compound 354 is added to the well. In FIG.18C, enzymes 356 are added to the well. In FIG. 18D, the fluorescentlabels still attached to the bottom of the well are imaged using, forexample, a line-scan confocal microscope schematically depicted aselement 380 to determine the activity of test compound 354.

In an alternative embodiment of the assay depicted in FIGS. 18A-18, theactivity of the test compound can be determined by comparing the imageobtained in FIG. 18D to the image obtained by imaging the fluorescenceof the fluorescent labels in FIG. 18A or 18B or the image of a controlwell.

Another example of an assay that may be performed according to thepresent invention is a tyrosine kinase assay. Tyrosine kinasesphosphorylate tyrosine residues of substrate peptides. The substratepeptide has both a tyrosine residue and a fluorescent tag. In thisassay, an antibody that at one end is selective for phosphorylatedtyrosine is bound at the other end to a surface such as a bead or thebottom of a well. Tyrosine kinase and a fluorescent-tagged peptide witha tyrosine residue are added to the well. If the tyrosine kinasephosphorylates the peptide, the phosphorylated tyrosine will bind to theantibody, thereby localizing the fluorescent tag on the surface to whichthe antibody is attached. If the tyrosine kinase does not phosphorylatethe peptide, the fluorescent tags on the peptides will be dispersedthroughout the well. The extent of phosphorylation of the peptide can bedetermined by measuring the fluorescence adjacent to the surface. Suchan assay can also be conducted where an antibody is used that isspecific to the fluorescent product produced by the action of the enzymeupon the fluorescent substrate.

In addition, live-cell enzyme assays can be performed according to thepresent invention. A number of techniques for investigating enzymaticactivity in live cells are known in the art (See Biochem. Histochem70,243 (1995), J. Fluorescence 3, 119 (1993)) as are substrates thatyield fluorescent products when acted on by enzymes (See Haugland R. P.Handbook of Fluorescent Probes and Research Chemical 6^(th) Ed. Chap.10). In general, these assays use probes that passively enter the celland are subsequently processed by intracellular enzymes to generateproducts retained within the cell. Other substrates yield insolublefluorescent products that precipitate at the site of enzymatic activity.The present invention can assay the degree of enzymatic activity anddetermine the precise spatial localization of the enzymatic activityusing such probes. Probes are available for assaying a wide variety ofenzymes using the present invention including but not limited tophosphatases, ATPases, 5′-nucleotidase, DNA and RNA polymerases,peptidases, proteases, esterases and peroxidase.

Enzyme activity assays can be performed according either the first orsecond experimental embodiments and the associated image analysisprotocols disclosed above.

Morphology

The methods of the present invention can also be used to perform assaysthat require a determination of cellular or sub-cellular morphology,including but not limited to axons and organelles. To perform suchassays, a fluorescent probe is introduced into the structure ofinterest, such as a cell or organelle, by direct micro-injection or bycontacting cells with cell-permeate reagents that are metabolized orotherwise altered so as to be retained in the structure of interest. Ifit is to be used with live cells, the fluorescent label must benon-toxic and biologically inert. Many appropriate dyes are availablecommercially (See Haugland R. P. Handbook of Fluorescent Probes andResearch Chemicals 6^(th) Ed. Chap. 15) for use in assays, for example,involving flow in capillaries, neuronal cell connectivity, translocationof dye through gap junctions, cell division and cell lysis and liposomefusion. In addition, these tracers can be used to track movement oflabeled cells in culture, tissues or intact organisms. Many techniquesemploying fluorescent tracers to assay cell or sub-cellular morphologyor movement are known in the art and may involve use of membranetracers, biotinylated dextran conjugators, fluorescent microspheres orproteins and protein conjugates (See Meth. Cell Biol. 29, 153 (1989);Cytometry 21. 230 (1995); Cell 84, 381 (1996); Biochem. Biophys. Acta988, 319 (1989); Cytometry 14, 747 (1993). The various embodiments ofthe present invention have significant advantages when used in thesetypes of assays. The present invention allows rapid imaging of multipleparameters with very fine spatial resolution.

Nucleic Acids

The present invention can also be used to conduct assays of nucleicacids. A specific DNA assay that would benefit from the spatialresolution and multi-wavelength imaging capability of the presentinvention is fluorescence-in-situ hybridization (FISH). FISH is animportant technique for localizing and determining the relativeabundance of specific nucleic acid sequences in cells, tissue,interphase nuclei and metaphase chromosomes and is used in clinicaldiagnostics and gene mapping (see Histo-chem J. 27, 4 (1995); Science247, 64 (1990); Trends Genet. 9, 71 (1993) and Science 250, 559 (1990)).A variety of fluorescent hybridization probes are available formulticolor fluorescent DNA and RNA hybridization techniques (seeHaugland R. P. Handbook of Fluorescent Probes and Research Chemicals,6^(th) Ed. Chap. 8.4). An additional technique determines chromosomebanding by the use of an AT or GC selective DNA-dyes with a nucleic acidcounter stain. This technique is widely used for karotype analysis andchromosome structure studies (see Human Genet. 57,1 (1981)).

Reactive Oxygen Species

The present invention can also be used to assay levels of variousreactive oxygen species such as singlet oxygen, superoxides and nitricoxide. The importance of these reactive oxygen species has only recentlybeen realized (See Biochem Pharmacol 47,373 (1994), J. Cell Biol. 126,901 (1994)). It is now known that singlet oxygen is responsible for muchof the physiological damage caused by reactive oxygen species (See J.Photochem. Photobiol. 11,241 (1991)). Nitric Oxide (NO), in particular,is now known to play a critical role as a molecular mediator in avariety of physiological processes including neurotransmission andblood-pressure regulation (See Current Biology 2,437 (1995), J. Med.Chem. 38,4343 (1995), Cell 78, 919 (1994)). Techniques are known in theart to perform assays to measure NO indirectly. For example, underphysiological conditions, NO is oxidized to nitrite and this can bedetected by monitoring absorbance at 548 nm or by use of a probe whichreacts with nitrite to form an identifiable fluorescent product. (SeeHaugland R. P., Handbook of Fluorescent Probes and Research Chemicals6^(th) Ed. Chap. 21).

pH

The present invention can also be used to perform assays involvingmeasurements of pH changes within cells or in cell-free media. Theimportance of the role of intracellular pH has been recognized in manydiverse physiological and pathological processes including cellproliferation, apoptosis, fertilization, malignancy, multi-drugresistance, ion transport, lysosomal storage disorders and Alzheimer'sdisease. (See Cell Physiol. Biochem. 2, 159 (1992); J. Biol. Chem. 270,6235 (1995); Biophys. J. 68, 739 (1995); J. Biol. Chem. 270, 19599(1995); Cancer Res. 54, 5670 (1994)). Fluorescent probes useful forassays of pH in the physiological range are available commercially (SeeHaugland R. P., Handbook of Fluorescent Probes and Research Chemicals6^(th) Ed. Chap. 23).

EXAMPLES

The invention described and claimed herein can be further appreciated byone skilled in the art through reference to the examples which follow.These examples are provided merely to illustrate several aspects of theinvention and shall not be construed to limit the invention in any way.

Transcription Factor Translocation

Cells were grown in 96-well plates, fixed, incubated withTexas-Red-labeled antibody to the transcription factor protein, rinsed,and then stained with 5 μM Hoechst 33342 in buffer.

The images in FIG. 19 are 0.5×0.5 mm² square with 1.08×1.08 μm²pixelation. Texas Red emission was excited at 568 nm and detected with a600-nm long pass filter. Hoechst emission was excited at 364 nm anddetected with a 420-480-nm bandpass filter. Image acquisition time was0.9 sec. There are ˜150 cells per image.

FIG. 19A is an image of a field of cells which were not activated beforefixing. The Texas Red intensity in the nucleus is low compared to thecytoplasm. FIG. 19B is the composite of the images in FIG. 19A and thatdue to the Hoechst 33342 emission.

FIG. 19C is an image of a field of cells which were activated prior tofixing. Due to color scaling, the cytoplasm is difficult to see withoutsaturating the nucleus. FIG. 19D is the composite of the images in FIG.19C and that due to the Hoechst 33342 emission from the same sample.

The data analysis was performed according to the following method. Thearea highlighted in FIG. 19B is reproduced in FIG. 20 which depicts themask generation steps. A binary representation of the Hoechst image wasgenerated by applying an appropriate threshold, those values greaterthan the threshold were set to one, those less than the threshold wereset to zero. This served as the primary mask. Two daughter masks werethen generated, one by eroding the primary mask, the other by dilatingthe primary mask and subtracting the original mask to form an annularmask. The Texas-Red-emission image was multiplied by the eroded binarymask, as depicted in FIG. 21, and the pixels summed as a measure of thequantity of labeled transcription factor in the nucleus. Similarly, theTexas-Red-emission image was multiplied by the annular binary mask, asdepicted in FIG. 21, and the pixels summed as a measure of the quantityof labeled transcription factor in the cytoplasm. The degree ofactivation is assessed using the ratio of nuclear to cytoplasmicintensity.

This ratio is represented in the bar graph in FIG. 28A for cells withand without activation.

Transient Ca Imaging of Muscarinic Receptor and Voltage-Gated ChannelStimulation

The cells in FIGS. 22 and 23 were from a neuroblastoma line. They weregrown and imaged in standard media. These cells express a muscarinicacetylcholine receptor that can be stimulated with Carbachol generatinga large intra-cellular Ca release as a second signal. In addition thecells express a voltage-gated “L” Ca channel which can be stimulated bydepolarizing the cell membrane with a large change in the external K⁺concentration and which can be inhibited with Verapamil.

In general, the image sequences were initiated by rapidly adding 100 μLof reagent in growth media to cells in 100 μL of growth media in a96-well plate. The turbulence caused by the added volume generates asmall distortion in cell shape. This distortion is visible as atransient alteration of the Ca fluorescence assigned to each cell in thefirst image frame after addition.

In FIG. 22 a movie with 1.2 seconds between frames is displayed. Theimage sequence was initiated by the rapid addition of 100 μM Carbachol.The final image is a binary mask, used to identify and enumeratefluorescent objects in the image, generated from the pre-injectionframe. Even though the pre-injection image appears dim, it is quitebright. The mask is applied to each image in the series, and for eachobject, the integrated intensity, normalized to the pre-injection image,is plotted vs. time, as displayed in FIG. 28B. The mask was notprocessed for overlapping cells. For example, object 1 is likely morethan one cell, but showed no response. Object 7 may be 2 overlappingcells, with one showing a delayed response.

FIG. 23A-H are selected frames of a movie showing the response of theneuroblastoma cells to a depolarization event initiated by the additionof 50 mM KCl which opens the voltage-gated “L” channels. The analysisprocedure was as is described above in connection to FIG. 28B. Theresults are displayed in FIG. 28C. Note the increased sensitivityobtained by using the “cell average” rather than the “image average”.

Live-Cell G-Protein Coupled Receptor Binding

The images displayed in FIGS. 24A-C to 25A-C were obtained on live cellsin 96-well plates. The cells had been transfected with a G-proteincoupled receptor, for which the natural peptide ligand is known. Priorto imaging, the cells were incubated with the native unlabeled ligand innormal growth media containing 10% serum for 20 minutes at 37° C.,followed by 20 minutes with 20 nM fluorescein-labeled ligand and 100 nMLDS 751, also at 37° C. Samples were not rinsed.

These images are (0.5×0.5) mm² are with (1.08×1.08) μm² pixelation.Fluorescein emission was excited at 488 nm and detected with a 45-nmbandpass filter centered at 535 nm. LDS 751 emission also excited at 488nm and was detected with a 40-nm bandpass filter, centered at 690 nm.Image acquisition time was 0.9 sec. These cells have ˜100,000receptors/cell or about 25 receptors/μm² of membrane surface.

FIG. 24A is an image of the cells after incubation with the labeledligand. No wash step was preformed prior to imaging. The substantialvariation in reception activity is evident. Some cells bind so littleligand that they appear as depressions in the background. A cell-by-cellanalysis of the binding activity is facilitated by making a mask from animage of LDS 751 emission, a non-specific nucleic acid stain, shown inFIG. 25B. The staining is not entirely uniform, but the vast majority ofcell volume is revealed. The overlay in FIG. 25C of the binary maskgenerated from thresholding the data in FIG. 25B with the receptorbinding image yields a pseudo-color map of receptor activity. Highactivity is represented as yellow, while low activity is shown asorange-red.

In FIG. 25 three images are displayed corresponding to points on thetitration curve of the 20-nM labeled ligand with the unlabeled ligand.The curve is displayed in FIG. 28D. A K_(i)=3±1×10¹⁰ M for the unlabeledligand is calculated.

Images illustrating receptor binding on a different mammalian cell lineare shown in FIG. 26A-D. FIG. 26A is an image of the cells incubatedwith a 256 nM Cy3-labeled ligand. A range of binding activity isvisible. FIG. 26B shows an overlay of the Cy3 data with a simultaneouslyacquired image of the 1-μM Hoechst 33342 stained nuclei. The latterserves as a reliable identifier of the individual cells. In FIG. 26C,the image is of the cells incubated with 256 nM Cy3-labeled ligand inthe presence of 10 μM unlabeled ligand, and in FIG. 26D, this data isdisplayed with the image of the 1-μM Hoechst 33342 stained nucleioverlaid. The effect of displaced fluid by unlabeled cells is evident inFIG. 26C. In the high correlation between FIGS. 26C and D exemplifiesthe effectiveness of identifying cells by their excluded volume.

Simulated Bead-Based Receptor-Binding

In FIG. 27A-D images of Cy5-labeled silica beads are presented. Theexperiment is a simulation of a receptor-binding assay in whichfluorescently-labeled ligands bind to membrane-bound receptors supportedon microspheres.

Silica microspheres, 4 μm in diameter, were coated with polyethylenimineand biotinylated with a biotin NHS-ester. The activity of the beads wasassayed with a fluorimeter by quantifying the amount of Cy5-labeledstreptavidin removed from solution by adsorption onto a known quantityof beads. Each bead was found to hold 1.3×10⁶ streptavidin molecules.Beads were loaded with a known quantity of Cy5 molecules by premixing anappropriate ratio of Cy5-labeled and non-labeled streptavidin andincubating with the beads. The loadings were equivalent to 0.16, 1.6 and16 fmole/200 μg of polystyrene beads. Each bead had an average of 17,170, or 1700 labels, respectively. The samples were placed in Costar96-well plates for imaging. Cy5 was excited with 647 nm laser light andthe emitted fluorescence was detected through a 40-nm bandpass filtercentered at 690 nm. The scanned images were acquired at 1-μm pixelationin approximately 0.7 seconds.

Beads loaded with 170 and 1700 molecules were readily detectable and the17-fluor beads are discernable in images constituting FIG. 27. Beadsloaded only with non-labeled streptavidin did riot produce appreciableintensities.

1-12. (canceled)
 13. A method of analyzing a biological sample,comprising the steps of: (a) providing a biological sample including atleast one target cell; (b) acquiring a digital image of the at least onetarget cell; (c) detecting a set of objects in the image; (d) copyingeach member of the detected set of objects into an extended bitmap witha border containing the object plus n extra pixels in each direction;(e) dilating each member of the set of objects from step (d); (f)comparing digital image of step (b) with the dilated bitmap of step (e)to generate an annular mask; (g) copying each member of the detected setof objects into another bitmap; (h) eroding each member of the set ofobjects from step (g) to generate an eroded bitmap; and (i) outputtingthe ratio of eroded-to-annular intensities for each member of thedetected set of objects.
 14. The method of claim 13, wherein thedetection step comprises thresholding.
 15. The method of claim 13,wherein outputting the ratio of eroded-to-annular intensities for eachmember of the detected set of objects comprises a graphicsuperimposition of the annular mask of step (f) and the eroded bitmap ofstep (g).
 16. The method of claim 13, wherein steps (b)-(i) areperformed on multiple target cells present in the biological sample. 17.The method of claim 16, wherein the multiple target cells comprise acluster of cells that are selected and identified with a boundary. 18.The method of claim 13, wherein acquiring step includes acquiring afirst digital image of a first labeled species and a second digitalimage of a second labeled species.
 19. The method of claim 18, whereinthe one or both of the labeled species are cellular components taggedwith a fluorescent label or a chromogenic label.
 20. The method of claim18, wherein the intensities of one or both of the labeled species iscalculated for all target cells in the image.
 21. The method of claim19, further comprising the step of determining the cellular location ofone or more of the cellular components tagged with a fluorescent label.22. A method of co-localizing cellular components, comprising the stepsof: (a) providing a biological sample including at least one targetcell; (b) acquiring a digital image of the at least one target cell; (c)detecting a set of objects in the image comprising a first labeledlocalized species; (d) copying each member of the detected set ofobjects into an extended bitmap with a border containing the object plusn extra pixels in each direction; (e) dilating each member of the set ofobjects from step (d); (f) acquiring a second digital image of the atleast one target cell comprising a second labeled localized species; and(g) superimposing the second digital image of step (f) onto the dilatedimage of step (e).
 23. The method of claim 22, wherein the first labeledlocalized species comprises a nuclear component tagged with a firstlabel and the second labeled localized species comprises a cytoplasmiccomponent tagged with a second label.
 24. The method of claim 22,wherein the data output includes one or more images showing cellularnuclear and cytoplasmic regions of the target cell.